diff --git a/.gitignore b/.gitignore index 2105788..b9a0c19 100644 --- a/.gitignore +++ b/.gitignore @@ -9,11 +9,13 @@ tmp/ *.cnt *.fq *.fasta +*.fastq +*.fastq.gz *.bt2 *.zip *.gz *.h5 - +*.bt2 tt/ .Rproj.user diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000..f66c11a --- /dev/null +++ b/.travis.yml @@ -0,0 +1,13 @@ +language: R +before_install: + - R --version + - RScript -e "library(knitr);" + - wget --version + - unzip --version + - wget --version + - unzip -h + - bowtie2 -h + - run_pipeline.pl -h + - pandoc --version + - module --version + diff --git a/00_AlignerIndices/load_data.sh b/00_AlignerIndices/load_data.sh new file mode 100755 index 0000000..8fd2873 --- /dev/null +++ b/00_AlignerIndices/load_data.sh @@ -0,0 +1,13 @@ +#!/bin/bash + +if [ -f /input/genomic/TrainingData/BBS/gbs_rmd/00_AlignerIndices/GBS_Workshop_Maize.zip ]; +then + echo "File found"; + unzip /input/genomic/TrainingData/BBS/gbs_rmd/00_AlignerIndices/GBS_Workshop_Maize.zip +else + echo "File not found. Downloading"; + wget -O GBS_Workshop_Maize.zip https://www.dropbox.com/sh/idwq4oo3uim31dw/AADW46CCFtxqnI4Kmjh_uAxoa?dl=1; + unzip GBS_Workshop_Maize.zip +fi + + diff --git a/00_AlignerIndices/run.R b/00_AlignerIndices/run.R new file mode 100644 index 0000000..cb30f28 --- /dev/null +++ b/00_AlignerIndices/run.R @@ -0,0 +1,4 @@ + +library(knitr) + +knit('run.Rmd') diff --git a/00_AlignerIndices/run.Rmd b/00_AlignerIndices/run.Rmd new file mode 100644 index 0000000..848eeff --- /dev/null +++ b/00_AlignerIndices/run.Rmd @@ -0,0 +1,13 @@ +# Download Maize Index from Dropbox + +- unzip index and delete zip afterwards +- convert mark down to html to load in browser + + +```{r test-bash, engine='bash'} + +./load_data.sh + +pandoc run.md -o run.html + +``` diff --git a/01_RawSequence/load_data.sh b/01_RawSequence/load_data.sh new file mode 100755 index 0000000..eded79b --- /dev/null +++ b/01_RawSequence/load_data.sh @@ -0,0 +1,14 @@ +#!/bin/bash + +rm -f C08L7ACXX_6_fastq.gz + +if [ -f /input/genomic/TrainingData/BBS/gbs_rmd/01_RawSequence/C08L7ACXX_6_fastq.gz ]; +then + echo "File found"; + ln -s /input/genomic/TrainingData/BBS/gbs_rmd/01_RawSequence/C08L7ACXX_6_fastq.gz +else + echo "File not found. Downloading"; + wget -O C08L7ACXX_6_fastq.gz "https://www.dropbox.com/s/vcrtcqunuxkwz90/C08L7ACXX_6_fastq.gz?dl=1"; +fi + + diff --git a/01_RawSequence/run.R b/01_RawSequence/run.R new file mode 100644 index 0000000..cb30f28 --- /dev/null +++ b/01_RawSequence/run.R @@ -0,0 +1,4 @@ + +library(knitr) + +knit('run.Rmd') diff --git a/01_RawSequence/run.Rmd b/01_RawSequence/run.Rmd new file mode 100644 index 0000000..5c0a914 --- /dev/null +++ b/01_RawSequence/run.Rmd @@ -0,0 +1,12 @@ +# Load data + +- linking data from input for convenience +- convert output to html for loading into the browser + + +```{r test-bash, engine='bash'} + +./load_data.sh +pandoc run.md -o run.html + +``` diff --git a/02_TagCounts/01_IndividualTagCounts/FastqToTagCounts.xml b/02_TagCounts/01_IndividualTagCounts/FastqToTagCounts.xml new file mode 100644 index 0000000..4a204d2 --- /dev/null +++ b/02_TagCounts/01_IndividualTagCounts/FastqToTagCounts.xml @@ -0,0 +1,14 @@ + + + + + ../../01_RawSequence/ + ./ + ../../50_KeyFiles/GBS_Workshop_Maize_key.txt + ApeKI + 3000000 + 1 + + + + diff --git a/02_TagCounts/01_IndividualTagCounts/run.R b/02_TagCounts/01_IndividualTagCounts/run.R new file mode 100644 index 0000000..cb30f28 --- /dev/null +++ b/02_TagCounts/01_IndividualTagCounts/run.R @@ -0,0 +1,4 @@ + +library(knitr) + +knit('run.Rmd') diff --git a/02_TagCounts/01_IndividualTagCounts/run.Rmd b/02_TagCounts/01_IndividualTagCounts/run.Rmd new file mode 100644 index 0000000..ced1d0e --- /dev/null +++ b/02_TagCounts/01_IndividualTagCounts/run.Rmd @@ -0,0 +1,9 @@ +# Count GBS tags + +```{r test-bash, engine='bash'} +module load tassel/3.0 +run_pipeline.pl -configFile FastqToTagCounts.xml +pandoc run.md -o run.html +module unload tassel/3.0 + +``` diff --git a/02_TagCounts/02_MergedTagCounts/MergeTagCounts.xml b/02_TagCounts/02_MergedTagCounts/MergeTagCounts.xml new file mode 100644 index 0000000..ed9c0e8 --- /dev/null +++ b/02_TagCounts/02_MergedTagCounts/MergeTagCounts.xml @@ -0,0 +1,11 @@ + + + + + ../01_IndividualTagCounts + ./GBS_Workshop_Maize.cnt + 5 + + + + diff --git a/02_TagCounts/02_MergedTagCounts/run.R b/02_TagCounts/02_MergedTagCounts/run.R new file mode 100644 index 0000000..cb30f28 --- /dev/null +++ b/02_TagCounts/02_MergedTagCounts/run.R @@ -0,0 +1,4 @@ + +library(knitr) + +knit('run.Rmd') diff --git a/02_TagCounts/02_MergedTagCounts/run.Rmd b/02_TagCounts/02_MergedTagCounts/run.Rmd new file mode 100644 index 0000000..fd23130 --- /dev/null +++ b/02_TagCounts/02_MergedTagCounts/run.Rmd @@ -0,0 +1,10 @@ +# Merge tag count files + +```{r test-bash, engine='bash'} +module load tassel/3.0 +run_pipeline.pl -configFile MergeTagCounts.xml +module unload tassel/3.0 + +pandoc run.md -o run.html + +``` diff --git a/02_TagCounts/03_TagCountToFastq/TagCountToFastq.xml b/02_TagCounts/03_TagCountToFastq/TagCountToFastq.xml new file mode 100644 index 0000000..10f5579 --- /dev/null +++ b/02_TagCounts/03_TagCountToFastq/TagCountToFastq.xml @@ -0,0 +1,11 @@ + + + + + ../02_MergedTagCounts/GBS_Workshop_Maize.cnt + ./GBS_Workshop_Maize.fq + 5 + + + + diff --git a/02_TagCounts/03_TagCountToFastq/run.R b/02_TagCounts/03_TagCountToFastq/run.R new file mode 100644 index 0000000..cb30f28 --- /dev/null +++ b/02_TagCounts/03_TagCountToFastq/run.R @@ -0,0 +1,4 @@ + +library(knitr) + +knit('run.Rmd') diff --git a/02_TagCounts/03_TagCountToFastq/run.Rmd b/02_TagCounts/03_TagCountToFastq/run.Rmd new file mode 100644 index 0000000..280784b --- /dev/null +++ b/02_TagCounts/03_TagCountToFastq/run.Rmd @@ -0,0 +1,11 @@ +# Convert to Fastq + +```{r test-bash, engine='bash'} + +module load tassel/3.0 +run_pipeline.pl -configFile TagCountToFastq.xml +module unload tassel/3.0 + +pandoc run.md -o run.html + +``` diff --git a/03_SAM/run.R b/03_SAM/run.R new file mode 100644 index 0000000..cb30f28 --- /dev/null +++ b/03_SAM/run.R @@ -0,0 +1,4 @@ + +library(knitr) + +knit('run.Rmd') diff --git a/03_SAM/run.Rmd b/03_SAM/run.Rmd new file mode 100644 index 0000000..54e3a71 --- /dev/null +++ b/03_SAM/run.Rmd @@ -0,0 +1,9 @@ +# Align GBS tags to reference genome + +```{r test-bash, engine='bash'} + +module load bowtie2/2.2.5 +bowtie2 -M 4 -p 15 --very-sensitive-local -x ../00_AlignerIndices/GBS_Workshop_Maize -U ../02_TagCounts/03_TagCountToFastq/GBS_Workshop_Maize.fq -S GBS_Workshop_Maize.sam +module unload bowtie2/2.2.5 + +``` diff --git a/04_TOPM/SAMConverter.xml b/04_TOPM/SAMConverter.xml new file mode 100644 index 0000000..a1878a8 --- /dev/null +++ b/04_TOPM/SAMConverter.xml @@ -0,0 +1,10 @@ + + + + + ../03_SAM/GBS_Workshop_Maize.sam + ./GBS_Workshop_Maize.topm + + + + diff --git a/04_TOPM/SAMConverter2.xml b/04_TOPM/SAMConverter2.xml new file mode 100644 index 0000000..e0fba24 --- /dev/null +++ b/04_TOPM/SAMConverter2.xml @@ -0,0 +1,10 @@ + + + + + <(samtools view -h ../03_SAM/GBS_Workshop_Maize.bam) + ./GBS_Workshop_Maize.topm + + + + diff --git a/04_TOPM/run.R b/04_TOPM/run.R new file mode 100644 index 0000000..cb30f28 --- /dev/null +++ b/04_TOPM/run.R @@ -0,0 +1,4 @@ + +library(knitr) + +knit('run.Rmd') diff --git a/04_TOPM/run.Rmd b/04_TOPM/run.Rmd new file mode 100644 index 0000000..ff9790e --- /dev/null +++ b/04_TOPM/run.Rmd @@ -0,0 +1,9 @@ +# Convert sam tags to tags on physical map (TOPM) + +```{r test-bash, engine='bash'} + +module load tassel/3.0 +run_pipeline.pl -configFile SAMConverter.xml +module unload tassel/3.0 + +``` diff --git a/05_TBT/01_IndividualTBT/SeqToTBTHDF5Plugin.xml b/05_TBT/01_IndividualTBT/SeqToTBTHDF5Plugin.xml new file mode 100644 index 0000000..827dff3 --- /dev/null +++ b/05_TBT/01_IndividualTBT/SeqToTBTHDF5Plugin.xml @@ -0,0 +1,15 @@ + + + + + ../../01_RawSequence + ../../50_KeyFiles/GBS_Workshop_Maize_key.txt + ApeKI + ./GBS_Workshop_Maize.h5 + 100000000 + GBS_Workshop_MaizeTBTHDF5_Log.txt + ../../02_TagCounts/02_MergedTagCounts/GBS_Workshop_Maize.cnt + + + + diff --git a/05_TBT/01_IndividualTBT/run.R b/05_TBT/01_IndividualTBT/run.R new file mode 100644 index 0000000..cb30f28 --- /dev/null +++ b/05_TBT/01_IndividualTBT/run.R @@ -0,0 +1,4 @@ + +library(knitr) + +knit('run.Rmd') diff --git a/05_TBT/01_IndividualTBT/run.Rmd b/05_TBT/01_IndividualTBT/run.Rmd new file mode 100644 index 0000000..addf5d3 --- /dev/null +++ b/05_TBT/01_IndividualTBT/run.Rmd @@ -0,0 +1,10 @@ +# Match tags to samples + + +```{r test-bash, engine='bash'} + +module load tassel/3.0 +run_pipeline.pl -configFile SeqToTBTHDF5Plugin.xml +module unload tassel/3.0 + +``` diff --git a/05_TBT/04_PivotMergedTaxaTBT/PivotTaxaTBTHDF5.xml b/05_TBT/04_PivotMergedTaxaTBT/PivotTaxaTBTHDF5.xml new file mode 100644 index 0000000..f7a8a72 --- /dev/null +++ b/05_TBT/04_PivotMergedTaxaTBT/PivotTaxaTBTHDF5.xml @@ -0,0 +1,12 @@ + + + + + ../01_IndividualTBT/GBS_Workshop_Maize.h5 +

./PivotTaxaTBTHDF5.h5

+ ./PivotTaxaTBTHDF5.log + + + + + diff --git a/05_TBT/04_PivotMergedTaxaTBT/run.R b/05_TBT/04_PivotMergedTaxaTBT/run.R new file mode 100644 index 0000000..cb30f28 --- /dev/null +++ b/05_TBT/04_PivotMergedTaxaTBT/run.R @@ -0,0 +1,4 @@ + +library(knitr) + +knit('run.Rmd') diff --git a/05_TBT/04_PivotMergedTaxaTBT/run.Rmd b/05_TBT/04_PivotMergedTaxaTBT/run.Rmd new file mode 100644 index 0000000..7a7a736 --- /dev/null +++ b/05_TBT/04_PivotMergedTaxaTBT/run.Rmd @@ -0,0 +1,10 @@ +# Pivot the tbt to prepare for SNP calling + + +```{r test-bash, engine='bash'} + +module load tassel/3.0 +run_pipeline.pl -configFile ./PivotTaxaTBTHDF5.xml +module unload tassel/3.0 + +``` diff --git a/06_HapMap/SNP_Caller.xml b/06_HapMap/SNP_Caller.xml new file mode 100644 index 0000000..93b6f17 --- /dev/null +++ b/06_HapMap/SNP_Caller.xml @@ -0,0 +1,16 @@ + + + + + ../05_TBT/04_PivotMergedTaxaTBT/PivotTaxaTBTHDF5.h5 + ./SNP_Caller + ../04_TOPM/GBS_Workshop_Maize.topm + 0.8 + 0.02 + 100000 + 9 + 10 + + + + diff --git a/06_HapMap/run.R b/06_HapMap/run.R new file mode 100644 index 0000000..cb30f28 --- /dev/null +++ b/06_HapMap/run.R @@ -0,0 +1,4 @@ + +library(knitr) + +knit('run.Rmd') diff --git a/06_HapMap/run.Rmd b/06_HapMap/run.Rmd new file mode 100644 index 0000000..f6adf8d --- /dev/null +++ b/06_HapMap/run.Rmd @@ -0,0 +1,23 @@ +# Call SNPs + + +```{r test-bash, engine='bash'} + +if [! -d /output/genomic/TrainingData/BBS/gbs_rmd/06_HapMap/SNP_Caller]; +then + mkdir -p /output/genomic/TrainingData/BBS/gbs_rmd/06_HapMap/SNP_Caller +fi + +if [! -L 06_HapMap]; +then + ln -s /output/genomic/TrainingData/BBS/gbs_rmd/06_HapMap +fi + +module load tassel/3.0 +run_pipeline.pl -configFile ./SNP_Caller.xml +module unload tassel/3.0 + +pandoc run.md -o run.html + + +``` diff --git a/50_KeyFiles/GBS_Workshop_Maize_key.txt b/50_KeyFiles/GBS_Workshop_Maize_key.txt new file mode 100755 index 0000000..2ac3d70 --- /dev/null +++ b/50_KeyFiles/GBS_Workshop_Maize_key.txt @@ -0,0 +1,193 @@ +Flowcell Lane Barcode DNASample LibraryPlate Row Col LibraryPrepID LibraryPlateID Enzyme BarcodeWell DNA_Plate SampleDNA_Well Genus Species Pedigree Population SeedLot FullSampleName +C05F2ACXX 5 CTCC B73 IBM94_lowvol_Ape A 1 250020986 450013677 ApeKI A01 IBM94 A01 zea mays B73:C05F2ACXX:5:250020986 +C05F2ACXX 5 TTCTC Mo17 IBM94_lowvol_Ape B 1 250020994 450013677 ApeKI B01 IBM94 B01 zea mays Mo17:C05F2ACXX:5:250020994 +C05F2ACXX 5 GCTTA M0034 IBM94_lowvol_Ape C 1 250021031 450013677 ApeKI C01 IBM94 C01 zea mays M0034:C05F2ACXX:5:250021031 +C05F2ACXX 5 AACGCCT M0035 IBM94_lowvol_Ape D 1 250021014 450013677 ApeKI D01 IBM94 D01 zea mays M0035:C05F2ACXX:5:250021014 +C05F2ACXX 5 AGGC M0077 IBM94_lowvol_Ape E 1 250021034 450013677 ApeKI E01 IBM94 E01 zea mays M0077:C05F2ACXX:5:250021034 +C05F2ACXX 5 TCGTT M0079 IBM94_lowvol_Ape F 1 250021046 450013677 ApeKI F01 IBM94 F01 zea mays M0079:C05F2ACXX:5:250021046 +C05F2ACXX 5 TGGCTA M0322 IBM94_lowvol_Ape G 1 250021058 450013677 ApeKI G01 IBM94 G01 zea mays M0322:C05F2ACXX:5:250021058 +C05F2ACXX 5 TGCTGGA M0323 IBM94_lowvol_Ape H 1 250021070 450013677 ApeKI H01 IBM94 H01 zea mays M0323:C05F2ACXX:5:250021070 +C05F2ACXX 5 TGCA M0001 IBM94_lowvol_Ape A 2 250020987 450013677 ApeKI A02 IBM94 A02 zea mays M0001:C05F2ACXX:5:250020987 +C05F2ACXX 5 AGCCC M0005 IBM94_lowvol_Ape B 2 250020995 450013677 ApeKI B02 IBM94 B02 zea mays M0005:C05F2ACXX:5:250020995 +C05F2ACXX 5 CTTCCA M0039 IBM94_lowvol_Ape C 2 250021003 450013677 ApeKI C02 IBM94 C02 zea mays M0039:C05F2ACXX:5:250021003 +C05F2ACXX 5 AATATGC M0040 IBM94_lowvol_Ape D 2 250021015 450013677 ApeKI D02 IBM94 D02 zea mays M0040:C05F2ACXX:5:250021015 +C05F2ACXX 5 GATC M0262 IBM94_lowvol_Ape E 2 250021035 450013677 ApeKI E02 IBM94 E02 zea mays M0262:C05F2ACXX:5:250021035 +C05F2ACXX 5 ACCTAA M0264 IBM94_lowvol_Ape F 2 250021047 450013677 ApeKI F02 IBM94 F02 zea mays M0264:C05F2ACXX:5:250021047 +C05F2ACXX 5 ACGTGTT M0325 IBM94_lowvol_Ape G 2 250021059 450013677 ApeKI G02 IBM94 G02 zea mays M0325:C05F2ACXX:5:250021059 +C05F2ACXX 5 AACCGAGA M0326 IBM94_lowvol_Ape H 2 250021071 450013677 ApeKI H02 IBM94 H02 zea mays M0326:C05F2ACXX:5:250021071 +C05F2ACXX 5 ACTA M0007 IBM94_lowvol_Ape A 3 250020988 450013677 ApeKI A03 IBM94 A03 zea mays M0007:C05F2ACXX:5:250020988 +C05F2ACXX 5 GTATT M0008 IBM94_lowvol_Ape B 3 250020996 450013677 ApeKI B03 IBM94 B03 zea mays M0008:C05F2ACXX:5:250020996 +C05F2ACXX 5 GAGATA M0043 IBM94_lowvol_Ape C 3 250021004 450013677 ApeKI C03 IBM94 C03 zea mays M0043:C05F2ACXX:5:250021004 +C05F2ACXX 5 ACGACTAC M0044 IBM94_lowvol_Ape D 3 250021016 450013677 ApeKI D03 IBM94 D03 zea mays M0044:C05F2ACXX:5:250021016 +C05F2ACXX 5 TCAC M0265 IBM94_lowvol_Ape E 3 250021036 450013677 ApeKI E03 IBM94 E03 zea mays M0265:C05F2ACXX:5:250021036 +C05F2ACXX 5 ATATGT M0266 IBM94_lowvol_Ape F 3 250021048 450013677 ApeKI F03 IBM94 F03 zea mays M0266:C05F2ACXX:5:250021048 +C05F2ACXX 5 ATTAATT M0328 IBM94_lowvol_Ape G 3 250021060 450013677 ApeKI G03 IBM94 G03 zea mays M0328:C05F2ACXX:5:250021060 +C05F2ACXX 5 ACAGGGAA M0337 IBM94_lowvol_Ape H 3 250021072 450013677 ApeKI H03 IBM94 H03 zea mays M0337:C05F2ACXX:5:250021072 +C05F2ACXX 5 CAGA M0010 IBM94_lowvol_Ape A 4 250021024 450013677 ApeKI A04 IBM94 A04 zea mays M0010:C05F2ACXX:5:250021024 +C05F2ACXX 5 CTGTA M0012 IBM94_lowvol_Ape B 4 250020997 450013677 ApeKI B04 IBM94 B04 zea mays M0012:C05F2ACXX:5:250020997 +C05F2ACXX 5 ATGCCT M0045 IBM94_lowvol_Ape C 4 250021005 450013677 ApeKI C04 IBM94 C04 zea mays M0045:C05F2ACXX:5:250021005 +C05F2ACXX 5 GGTGT M0046 IBM94_lowvol_Ape D 4 250021032 450013677 ApeKI D04 IBM94 D04 zea mays M0046:C05F2ACXX:5:250021032 +C05F2ACXX 5 AGGAT M0267 IBM94_lowvol_Ape E 4 250021037 450013677 ApeKI E04 IBM94 E04 zea mays M0267:C05F2ACXX:5:250021037 +C05F2ACXX 5 ATCGTA M0269 IBM94_lowvol_Ape F 4 250021049 450013677 ApeKI F04 IBM94 F04 zea mays M0269:C05F2ACXX:5:250021049 +C05F2ACXX 5 ATTGGAT M0341 IBM94_lowvol_Ape G 4 250021061 450013677 ApeKI G04 IBM94 G04 zea mays M0341:C05F2ACXX:5:250021061 +C05F2ACXX 5 ACGTGGTA M0344 IBM94_lowvol_Ape H 4 250021073 450013677 ApeKI H04 IBM94 H04 zea mays M0344:C05F2ACXX:5:250021073 +C05F2ACXX 5 AACT M0014 IBM94_lowvol_Ape A 5 250021025 450013677 ApeKI A05 IBM94 A05 zea mays M0014:C05F2ACXX:5:250021025 +C05F2ACXX 5 ACCGT M0015 IBM94_lowvol_Ape B 5 250021028 450013677 ApeKI B05 IBM94 B05 zea mays M0015:C05F2ACXX:5:250021028 +C05F2ACXX 5 TATTTTT M0048 IBM94_lowvol_Ape C 5 250021006 450013677 ApeKI C05 IBM94 C05 zea mays M0048:C05F2ACXX:5:250021006 +C05F2ACXX 5 TAGCATGC M0051 IBM94_lowvol_Ape D 5 250021017 450013677 ApeKI D05 IBM94 D05 zea mays M0051:C05F2ACXX:5:250021017 +C05F2ACXX 5 ATTGA M0272 IBM94_lowvol_Ape E 5 250021038 450013677 ApeKI E05 IBM94 E05 zea mays M0272:C05F2ACXX:5:250021038 +C05F2ACXX 5 CATCGT M0275 IBM94_lowvol_Ape F 5 250021050 450013677 ApeKI F05 IBM94 F05 zea mays M0275:C05F2ACXX:5:250021050 +C05F2ACXX 5 CATAAGT M0345 IBM94_lowvol_Ape G 5 250021062 450013677 ApeKI G05 IBM94 G05 zea mays M0345:C05F2ACXX:5:250021062 +C05F2ACXX 5 CCATGGGT M0346 IBM94_lowvol_Ape H 5 250021074 450013677 ApeKI H05 IBM94 H05 zea mays M0346:C05F2ACXX:5:250021074 +C05F2ACXX 5 GCGT M0016 IBM94_lowvol_Ape A 6 250020989 450013677 ApeKI A06 IBM94 A06 zea mays M0016:C05F2ACXX:5:250020989 +C05F2ACXX 5 GTAA M0017 IBM94_lowvol_Ape B 6 250021029 450013677 ApeKI B06 IBM94 B06 zea mays M0017:C05F2ACXX:5:250021029 +C05F2ACXX 5 CTTGCTT M0052 IBM94_lowvol_Ape C 6 250021007 450013677 ApeKI C06 IBM94 C06 zea mays M0052:C05F2ACXX:5:250021007 +C05F2ACXX 5 AGTGGA M0054 IBM94_lowvol_Ape D 6 250021033 450013677 ApeKI D06 IBM94 D06 zea mays M0054:C05F2ACXX:5:250021033 +C05F2ACXX 5 CATCT M0276 IBM94_lowvol_Ape E 6 250021039 450013677 ApeKI E06 IBM94 E06 zea mays M0276:C05F2ACXX:5:250021039 +C05F2ACXX 5 CGCGGT M0281 IBM94_lowvol_Ape F 6 250021051 450013677 ApeKI F06 IBM94 F06 zea mays M0281:C05F2ACXX:5:250021051 +C05F2ACXX 5 CGCTGAT M0352 IBM94_lowvol_Ape G 6 250021063 450013677 ApeKI G06 IBM94 G06 zea mays M0352:C05F2ACXX:5:250021063 +C05F2ACXX 5 CGCGGAGA M0354 IBM94_lowvol_Ape H 6 250021075 450013677 ApeKI H06 IBM94 H06 zea mays M0354:C05F2ACXX:5:250021075 +C05F2ACXX 5 TGCGA M0021 IBM94_lowvol_Ape A 7 250021026 450013677 ApeKI A07 IBM94 A07 zea mays M0021:C05F2ACXX:5:250021026 +C05F2ACXX 5 GGTTGT M0022 IBM94_lowvol_Ape B 7 250021030 450013677 ApeKI B07 IBM94 B07 zea mays M0022:C05F2ACXX:5:250021030 +C05F2ACXX 5 ATGAAAC M0055 IBM94_lowvol_Ape C 7 250021008 450013677 ApeKI C07 IBM94 C07 zea mays M0055:C05F2ACXX:5:250021008 +C05F2ACXX 5 TAGGCCAT M0057 IBM94_lowvol_Ape D 7 250021018 450013677 ApeKI D07 IBM94 D07 zea mays M0057:C05F2ACXX:5:250021018 +C05F2ACXX 5 CCTAC M0284 IBM94_lowvol_Ape E 7 250021040 450013677 ApeKI E07 IBM94 E07 zea mays M0284:C05F2ACXX:5:250021040 +C05F2ACXX 5 CTATTA M0287 IBM94_lowvol_Ape F 7 250021052 450013677 ApeKI F07 IBM94 F07 zea mays M0287:C05F2ACXX:5:250021052 +C05F2ACXX 5 CGGTAGA M0355 IBM94_lowvol_Ape G 7 250021064 450013677 ApeKI G07 IBM94 G07 zea mays M0355:C05F2ACXX:5:250021064 +C05F2ACXX 5 CGTGTGGT M0357 IBM94_lowvol_Ape H 7 250021076 450013677 ApeKI H07 IBM94 H07 zea mays M0357:C05F2ACXX:5:250021076 +C05F2ACXX 5 CGAT M0023 IBM94_lowvol_Ape A 8 250020990 450013677 ApeKI A08 IBM94 A08 zea mays M0023:C05F2ACXX:5:250020990 +C05F2ACXX 5 CCAGCT M0024 IBM94_lowvol_Ape B 8 250020998 450013677 ApeKI B08 IBM94 B08 zea mays M0024:C05F2ACXX:5:250020998 +C05F2ACXX 5 AAAAGTT M0058 IBM94_lowvol_Ape C 8 250021009 450013677 ApeKI C08 IBM94 C08 zea mays M0058:C05F2ACXX:5:250021009 +C05F2ACXX 5 TGCAAGGA M0060 IBM94_lowvol_Ape D 8 250021019 450013677 ApeKI D08 IBM94 D08 zea mays M0060:C05F2ACXX:5:250021019 +C05F2ACXX 5 GAGGA M0288 IBM94_lowvol_Ape E 8 250021041 450013677 ApeKI E08 IBM94 E08 zea mays M0288:C05F2ACXX:5:250021041 +C05F2ACXX 5 GCCAGT M0296 IBM94_lowvol_Ape F 8 250021053 450013677 ApeKI F08 IBM94 F08 zea mays M0296:C05F2ACXX:5:250021053 +C05F2ACXX 5 CTACGGA M0360 IBM94_lowvol_Ape G 8 250021065 450013677 ApeKI G08 IBM94 G08 zea mays M0360:C05F2ACXX:5:250021065 +C05F2ACXX 5 GCTGTGGA M0364 IBM94_lowvol_Ape H 8 250021077 450013677 ApeKI H08 IBM94 H08 zea mays M0364:C05F2ACXX:5:250021077 +C05F2ACXX 5 CGCTT M0025 IBM94_lowvol_Ape A 9 250021027 450013677 ApeKI A09 IBM94 A09 zea mays M0025:C05F2ACXX:5:250021027 +C05F2ACXX 5 TTCAGA M0027 IBM94_lowvol_Ape B 9 250020999 450013677 ApeKI B09 IBM94 B09 zea mays M0027:C05F2ACXX:5:250020999 +C05F2ACXX 5 GAATTCA M0061 IBM94_lowvol_Ape C 9 250021010 450013677 ApeKI C09 IBM94 C09 zea mays M0061:C05F2ACXX:5:250021010 +C05F2ACXX 5 TGGTACGT M0062 IBM94_lowvol_Ape D 9 250021020 450013677 ApeKI D09 IBM94 D09 zea mays M0062:C05F2ACXX:5:250021020 +C05F2ACXX 5 GGAAC M0297 IBM94_lowvol_Ape E 9 250021042 450013677 ApeKI E09 IBM94 E09 zea mays M0297:C05F2ACXX:5:250021042 +C05F2ACXX 5 GGAAGA M0298 IBM94_lowvol_Ape F 9 250021054 450013677 ApeKI F09 IBM94 F09 zea mays M0298:C05F2ACXX:5:250021054 +C05F2ACXX 5 GCGGAAT M0365 IBM94_lowvol_Ape G 9 250021066 450013677 ApeKI G09 IBM94 G09 zea mays M0365:C05F2ACXX:5:250021066 +C05F2ACXX 5 GGATTGGT M0368 IBM94_lowvol_Ape H 9 250021078 450013677 ApeKI H09 IBM94 H09 zea mays M0368:C05F2ACXX:5:250021078 +C05F2ACXX 5 TCACC M0028 IBM94_lowvol_Ape A 10 250020991 450013677 ApeKI A10 IBM94 A10 zea mays M0028:C05F2ACXX:5:250020991 +C05F2ACXX 5 TAGGAA M0029 IBM94_lowvol_Ape B 10 250021000 450013677 ApeKI B10 IBM94 B10 zea mays M0029:C05F2ACXX:5:250021000 +C05F2ACXX 5 GAACTTC M0063 IBM94_lowvol_Ape C 10 250021011 450013677 ApeKI C10 IBM94 C10 zea mays M0063:C05F2ACXX:5:250021011 +C05F2ACXX 5 TCTCAGTC M0066 IBM94_lowvol_Ape D 10 250021021 450013677 ApeKI D10 IBM94 D10 zea mays M0066:C05F2ACXX:5:250021021 +C05F2ACXX 5 GTCAA M0309 IBM94_lowvol_Ape E 10 250021043 450013677 ApeKI E10 IBM94 E10 zea mays M0309:C05F2ACXX:5:250021043 +C05F2ACXX 5 GTACTT M0310 IBM94_lowvol_Ape F 10 250021055 450013677 ApeKI F10 IBM94 F10 zea mays M0310:C05F2ACXX:5:250021055 +C05F2ACXX 5 TAGCGGA M0369 IBM94_lowvol_Ape G 10 250021067 450013677 ApeKI G10 IBM94 G10 zea mays M0369:C05F2ACXX:5:250021067 +C05F2ACXX 5 GTGAGGGT M0378 IBM94_lowvol_Ape H 10 250021079 450013677 ApeKI H10 IBM94 H10 zea mays M0378:C05F2ACXX:5:250021079 +C05F2ACXX 5 CTAGC M0030 IBM94_lowvol_Ape A 11 250020992 450013677 ApeKI A11 IBM94 A11 zea mays M0030:C05F2ACXX:5:250020992 +C05F2ACXX 5 GCTCTA M0031 IBM94_lowvol_Ape B 11 250021001 450013677 ApeKI B11 IBM94 B11 zea mays M0031:C05F2ACXX:5:250021001 +C05F2ACXX 5 GGACCTA M0067 IBM94_lowvol_Ape C 11 250021012 450013677 ApeKI C11 IBM94 C11 zea mays M0067:C05F2ACXX:5:250021012 +C05F2ACXX 5 CCGGATAT M0074 IBM94_lowvol_Ape D 11 250021022 450013677 ApeKI D11 IBM94 D11 zea mays M0074:C05F2ACXX:5:250021022 +C05F2ACXX 5 TAATA M0311 IBM94_lowvol_Ape E 11 250021044 450013677 ApeKI E11 IBM94 E11 zea mays M0311:C05F2ACXX:5:250021044 +C05F2ACXX 5 GTTGAA M0315 IBM94_lowvol_Ape F 11 250021056 450013677 ApeKI F11 IBM94 F11 zea mays M0315:C05F2ACXX:5:250021056 +C05F2ACXX 5 TCGAAGA M0379 IBM94_lowvol_Ape G 11 250021068 450013677 ApeKI G11 IBM94 G11 zea mays M0379:C05F2ACXX:5:250021068 +C05F2ACXX 5 TATCGGGA M0382 IBM94_lowvol_Ape H 11 250021080 450013677 ApeKI H11 IBM94 H11 zea mays M0382:C05F2ACXX:5:250021080 +C05F2ACXX 5 ACAAA M0032 IBM94_lowvol_Ape A 12 250020993 450013677 ApeKI A12 IBM94 A12 zea mays M0032:C05F2ACXX:5:250020993 +C05F2ACXX 5 CCACAA M0033 IBM94_lowvol_Ape B 12 250021002 450013677 ApeKI B12 IBM94 B12 zea mays M0033:C05F2ACXX:5:250021002 +C05F2ACXX 5 GTCGATT M0075 IBM94_lowvol_Ape C 12 250021013 450013677 ApeKI C12 IBM94 C12 zea mays M0075:C05F2ACXX:5:250021013 +C05F2ACXX 5 CGCCTTAT M0076 IBM94_lowvol_Ape D 12 250021023 450013677 ApeKI D12 IBM94 D12 zea mays M0076:C05F2ACXX:5:250021023 +C05F2ACXX 5 TACAT M0317 IBM94_lowvol_Ape E 12 250021045 450013677 ApeKI E12 IBM94 E12 zea mays M0317:C05F2ACXX:5:250021045 +C05F2ACXX 5 TAACGA M0321 IBM94_lowvol_Ape F 12 250021057 450013677 ApeKI F12 IBM94 F12 zea mays M0321:C05F2ACXX:5:250021057 +C05F2ACXX 5 TCTGTGA M0383 IBM94_lowvol_Ape G 12 250021069 450013677 ApeKI G12 IBM94 G12 zea mays M0383:C05F2ACXX:5:250021069 +C05F2ACXX 5 TTCCTGGA M0384 IBM94_lowvol_Ape H 12 250021081 450013677 ApeKI H12 IBM94 H12 zea mays M0384:C05F2ACXX:5:250021081 +C08L7ACXX 6 CTCC DE_2 MGP1_low_vol A 1 250047921 450014183 ApeKI A01 MGP1 A01 zea mays DE_2:C08L7ACXX:6:250047921 +C08L7ACXX 6 TTCTC EMPTY MGP1_low_vol B 1 250047922 450014183 ApeKI B01 MGP1 B01 zea mays EMPTY:C08L7ACXX:6:250047922 +C08L7ACXX 6 GCTTA NC250 MGP1_low_vol C 1 250047923 450014183 ApeKI C01 MGP1 C01 zea mays NC250:C08L7ACXX:6:250047923 +C08L7ACXX 6 AACGCCT B109 MGP1_low_vol D 1 250047924 450014183 ApeKI D01 MGP1 D01 zea mays B109:C08L7ACXX:6:250047924 +C08L7ACXX 6 AGGC B73Htrhm MGP1_low_vol E 1 250047925 450014183 ApeKI E01 MGP1 E01 zea mays B73Htrhm:C08L7ACXX:6:250047925 +C08L7ACXX 6 TCGTT R109B MGP1_low_vol F 1 250047926 450014183 ApeKI F01 MGP1 F01 zea mays R109B:C08L7ACXX:6:250047926 +C08L7ACXX 6 TGGCTA CM174 MGP1_low_vol G 1 250047927 450014183 ApeKI G01 MGP1 G01 zea mays CM174:C08L7ACXX:6:250047927 +C08L7ACXX 6 TGCTGGA CML281 MGP1_low_vol H 1 250047928 450014183 ApeKI H01 MGP1 H01 zea mays CML281:C08L7ACXX:6:250047928 +C08L7ACXX 6 TGCA R168 MGP1_low_vol A 2 250047929 450014183 ApeKI A02 MGP1 A02 zea mays R168:C08L7ACXX:6:250047929 +C08L7ACXX 6 AGCCC A239 MGP1_low_vol B 2 250047930 450014183 ApeKI B02 MGP1 B02 zea mays A239:C08L7ACXX:6:250047930 +C08L7ACXX 6 CTTCCA A680 MGP1_low_vol C 2 250047931 450014183 ApeKI C02 MGP1 C02 zea mays A680:C08L7ACXX:6:250047931 +C08L7ACXX 6 AATATGC NC328 MGP1_low_vol D 2 250047932 450014183 ApeKI D02 MGP1 D02 zea mays NC328:C08L7ACXX:6:250047932 +C08L7ACXX 6 GATC CH701-30 MGP1_low_vol E 2 250047933 450014183 ApeKI E02 MGP1 E02 zea mays CH701-30:C08L7ACXX:6:250047933 +C08L7ACXX 6 ACCTAA CML228 MGP1_low_vol F 2 250047934 450014183 ApeKI F02 MGP1 F02 zea mays CML228:C08L7ACXX:6:250047934 +C08L7ACXX 6 ACGTGTT WD MGP1_low_vol G 2 250047935 450014183 ApeKI G02 MGP1 G02 zea mays WD:C08L7ACXX:6:250047935 +C08L7ACXX 6 AACCGAGA DE_3 MGP1_low_vol H 2 250047936 450014183 ApeKI H02 MGP1 H02 zea mays DE_3:C08L7ACXX:6:250047936 +C08L7ACXX 6 ACTA NC290A MGP1_low_vol A 3 250047937 450014183 ApeKI A03 MGP1 A03 zea mays NC290A:C08L7ACXX:6:250047937 +C08L7ACXX 6 GTATT B104 MGP1_low_vol B 3 250047938 450014183 ApeKI B03 MGP1 B03 zea mays B104:C08L7ACXX:6:250047938 +C08L7ACXX 6 GAGATA NC356 MGP1_low_vol C 3 250047939 450014183 ApeKI C03 MGP1 C03 zea mays NC356:C08L7ACXX:6:250047939 +C08L7ACXX 6 ACGACTAC A619 MGP1_low_vol D 3 250047940 450014183 ApeKI D03 MGP1 D03 zea mays A619:C08L7ACXX:6:250047940 +C08L7ACXX 6 TCAC CML287 MGP1_low_vol E 3 250047941 450014183 ApeKI E03 MGP1 E03 zea mays CML287:C08L7ACXX:6:250047941 +C08L7ACXX 6 ATATGT CML92 MGP1_low_vol F 3 250047942 450014183 ApeKI F03 MGP1 F03 zea mays CML92:C08L7ACXX:6:250047942 +C08L7ACXX 6 ATTAATT Ki14 MGP1_low_vol G 3 250047943 450014183 ApeKI G03 MGP1 G03 zea mays Ki14:C08L7ACXX:6:250047943 +C08L7ACXX 6 ACAGGGAA L317 MGP1_low_vol H 3 250047944 450014183 ApeKI H03 MGP1 H03 zea mays L317:C08L7ACXX:6:250047944 +C08L7ACXX 6 CAGA CML14 MGP1_low_vol A 4 250047945 450014183 ApeKI A04 MGP1 A04 zea mays CML14:C08L7ACXX:6:250047945 +C08L7ACXX 6 CTGTA NC230 MGP1_low_vol B 4 250047946 450014183 ApeKI B04 MGP1 B04 zea mays NC230:C08L7ACXX:6:250047946 +C08L7ACXX 6 ATGCCT CI28A MGP1_low_vol C 4 250047947 450014183 ApeKI C04 MGP1 C04 zea mays CI28A:C08L7ACXX:6:250047947 +C08L7ACXX 6 GGTGT NC262 MGP1_low_vol D 4 250047948 450014183 ApeKI D04 MGP1 D04 zea mays NC262:C08L7ACXX:6:250047948 +C08L7ACXX 6 AGGAT W117Ht MGP1_low_vol E 4 250047949 450014183 ApeKI E04 MGP1 E04 zea mays W117Ht:C08L7ACXX:6:250047949 +C08L7ACXX 6 ATCGTA A632 MGP1_low_vol F 4 250047950 450014183 ApeKI F04 MGP1 F04 zea mays A632:C08L7ACXX:6:250047950 +C08L7ACXX 6 ATTGGAT CML45 MGP1_low_vol G 4 250047951 450014183 ApeKI G04 MGP1 G04 zea mays CML45:C08L7ACXX:6:250047951 +C08L7ACXX 6 ACGTGGTA CI3A MGP1_low_vol H 4 250047952 450014183 ApeKI H04 MGP1 H04 zea mays CI3A:C08L7ACXX:6:250047952 +C08L7ACXX 6 AACT NC338 MGP1_low_vol A 5 250047953 450014183 ApeKI A05 MGP1 A05 zea mays NC338:C08L7ACXX:6:250047953 +C08L7ACXX 6 ACCGT A272 MGP1_low_vol B 5 250047954 450014183 ApeKI B05 MGP1 B05 zea mays A272:C08L7ACXX:6:250047954 +C08L7ACXX 6 TATTTTT Va59 MGP1_low_vol C 5 250047955 450014183 ApeKI C05 MGP1 C05 zea mays Va59:C08L7ACXX:6:250047955 +C08L7ACXX 6 TAGCATGC B103 MGP1_low_vol D 5 250047956 450014183 ApeKI D05 MGP1 D05 zea mays B103:C08L7ACXX:6:250047956 +C08L7ACXX 6 ATTGA A682 MGP1_low_vol E 5 250047957 450014183 ApeKI E05 MGP1 E05 zea mays A682:C08L7ACXX:6:250047957 +C08L7ACXX 6 CATCGT Sg18 MGP1_low_vol F 5 250047958 450014183 ApeKI F05 MGP1 F05 zea mays Sg18:C08L7ACXX:6:250047958 +C08L7ACXX 6 CATAAGT NC368 MGP1_low_vol G 5 250047959 450014183 ApeKI G05 MGP1 G05 zea mays NC368:C08L7ACXX:6:250047959 +C08L7ACXX 6 CCATGGGT Os420 MGP1_low_vol H 5 250047960 450014183 ApeKI H05 MGP1 H05 zea mays Os420:C08L7ACXX:6:250047960 +C08L7ACXX 6 GCGT CO106 MGP1_low_vol A 6 250047961 450014183 ApeKI A06 MGP1 A06 zea mays CO106:C08L7ACXX:6:250047961 +C08L7ACXX 6 GTAA CML258 MGP1_low_vol B 6 250047962 450014183 ApeKI B06 MGP1 B06 zea mays CML258:C08L7ACXX:6:250047962 +C08L7ACXX 6 CTTGCTT A554 MGP1_low_vol C 6 250047963 450014183 ApeKI C06 MGP1 C06 zea mays A554:C08L7ACXX:6:250047963 +C08L7ACXX 6 AGTGGA F6 MGP1_low_vol D 6 250047964 450014183 ApeKI D06 MGP1 D06 zea mays F6:C08L7ACXX:6:250047964 +C08L7ACXX 6 CATCT Tzi25 MGP1_low_vol E 6 250047965 450014183 ApeKI E06 MGP1 E06 zea mays Tzi25:C08L7ACXX:6:250047965 +C08L7ACXX 6 CGCGGT CML277 MGP1_low_vol F 6 250047966 450014183 ApeKI F06 MGP1 F06 zea mays CML277:C08L7ACXX:6:250047966 +C08L7ACXX 6 CGCTGAT NC320 MGP1_low_vol G 6 250047967 450014183 ApeKI G06 MGP1 G06 zea mays NC320:C08L7ACXX:6:250047967 +C08L7ACXX 6 CGCGGAGA CML323 MGP1_low_vol H 6 250047968 450014183 ApeKI H06 MGP1 H06 zea mays CML323:C08L7ACXX:6:250047968 +C08L7ACXX 6 TGCGA W22 MGP1_low_vol A 7 250047969 450014183 ApeKI A07 MGP1 A07 zea mays W22:C08L7ACXX:6:250047969 +C08L7ACXX 6 GGTTGT B97 MGP1_low_vol B 7 250047970 450014183 ApeKI B07 MGP1 B07 zea mays B97:C08L7ACXX:6:250047970 +C08L7ACXX 6 ATGAAAC NC298 MGP1_low_vol C 7 250047971 450014183 ApeKI C07 MGP1 C07 zea mays NC298:C08L7ACXX:6:250047971 +C08L7ACXX 6 TAGGCCAT Oh603 MGP1_low_vol D 7 250047972 450014183 ApeKI D07 MGP1 D07 zea mays Oh603:C08L7ACXX:6:250047972 +C08L7ACXX 6 CCTAC Oh43E MGP1_low_vol E 7 250047973 450014183 ApeKI E07 MGP1 E07 zea mays Oh43E:C08L7ACXX:6:250047973 +C08L7ACXX 6 CTATTA Va35 MGP1_low_vol F 7 250047974 450014183 ApeKI F07 MGP1 F07 zea mays Va35:C08L7ACXX:6:250047974 +C08L7ACXX 6 CGGTAGA CO125 MGP1_low_vol G 7 250047975 450014183 ApeKI G07 MGP1 G07 zea mays CO125:C08L7ACXX:6:250047975 +C08L7ACXX 6 CGTGTGGT NC364 MGP1_low_vol H 7 250047976 450014183 ApeKI H07 MGP1 H07 zea mays NC364:C08L7ACXX:6:250047976 +C08L7ACXX 6 CGAT M14 MGP1_low_vol A 8 250047977 450014183 ApeKI A08 MGP1 A08 zea mays M14:C08L7ACXX:6:250047977 +C08L7ACXX 6 CCAGCT SC213R MGP1_low_vol B 8 250047978 450014183 ApeKI B08 MGP1 B08 zea mays SC213R:C08L7ACXX:6:250047978 +C08L7ACXX 6 AAAAGTT H91 MGP1_low_vol C 8 250047979 450014183 ApeKI C08 MGP1 C08 zea mays H91:C08L7ACXX:6:250047979 +C08L7ACXX 6 TGCAAGGA Oh40B MGP1_low_vol D 8 250047980 450014183 ApeKI D08 MGP1 D08 zea mays Oh40B:C08L7ACXX:6:250047980 +C08L7ACXX 6 GAGGA CI.7 MGP1_low_vol E 8 250047981 450014183 ApeKI E08 MGP1 E08 zea mays CI.7:C08L7ACXX:6:250047981 +C08L7ACXX 6 GCCAGT NC300 MGP1_low_vol F 8 250047982 450014183 ApeKI F08 MGP1 F08 zea mays NC300:C08L7ACXX:6:250047982 +C08L7ACXX 6 CTACGGA CI66 MGP1_low_vol G 8 250047983 450014183 ApeKI G08 MGP1 G08 zea mays CI66:C08L7ACXX:6:250047983 +C08L7ACXX 6 GCTGTGGA 33-16 MGP1_low_vol H 8 250047984 450014183 ApeKI H08 MGP1 H08 zea mays 33-16:C08L7ACXX:6:250047984 +C08L7ACXX 6 CGCTT CML220 MGP1_low_vol A 9 250047985 450014183 ApeKI A09 MGP1 A09 zea mays CML220:C08L7ACXX:6:250047985 +C08L7ACXX 6 TTCAGA K55 MGP1_low_vol B 9 250047986 450014183 ApeKI B09 MGP1 B09 zea mays K55:C08L7ACXX:6:250047986 +C08L7ACXX 6 GAATTCA CML52 MGP1_low_vol C 9 250047987 450014183 ApeKI C09 MGP1 C09 zea mays CML52:C08L7ACXX:6:250047987 +C08L7ACXX 6 TGGTACGT CML333 MGP1_low_vol D 9 250047988 450014183 ApeKI D09 MGP1 D09 zea mays CML333:C08L7ACXX:6:250047988 +C08L7ACXX 6 GGAAC NC318 MGP1_low_vol E 9 250047989 450014183 ApeKI E09 MGP1 E09 zea mays NC318:C08L7ACXX:6:250047989 +C08L7ACXX 6 GGAAGA Ki11 MGP1_low_vol F 9 250047990 450014183 ApeKI F09 MGP1 F09 zea mays Ki11:C08L7ACXX:6:250047990 +C08L7ACXX 6 GCGGAAT B10 MGP1_low_vol G 9 250047991 450014183 ApeKI G09 MGP1 G09 zea mays B10:C08L7ACXX:6:250047991 +C08L7ACXX 6 GGATTGGT CML238 MGP1_low_vol H 9 250047992 450014183 ApeKI H09 MGP1 H09 zea mays CML238:C08L7ACXX:6:250047992 +C08L7ACXX 6 TCACC B84 MGP1_low_vol A 10 250047993 450014183 ApeKI A10 MGP1 A10 zea mays B84:C08L7ACXX:6:250047993 +C08L7ACXX 6 TAGGAA B76 MGP1_low_vol B 10 250047994 450014183 ApeKI B10 MGP1 B10 zea mays B76:C08L7ACXX:6:250047994 +C08L7ACXX 6 GAACTTC Pa875 MGP1_low_vol C 10 250047995 450014183 ApeKI C10 MGP1 C10 zea mays Pa875:C08L7ACXX:6:250047995 +C08L7ACXX 6 TCTCAGTC CML332 MGP1_low_vol D 10 250047996 450014183 ApeKI D10 MGP1 D10 zea mays CML332:C08L7ACXX:6:250047996 +C08L7ACXX 6 GTCAA CM105 MGP1_low_vol E 10 250047997 450014183 ApeKI E10 MGP1 E10 zea mays CM105:C08L7ACXX:6:250047997 +C08L7ACXX 6 GTACTT B77 MGP1_low_vol F 10 250047998 450014183 ApeKI F10 MGP1 F10 zea mays B77:C08L7ACXX:6:250047998 +C08L7ACXX 6 TAGCGGA I29 MGP1_low_vol G 10 250047999 450014183 ApeKI G10 MGP1 G10 zea mays I29:C08L7ACXX:6:250047999 +C08L7ACXX 6 GTGAGGGT I137TN MGP1_low_vol H 10 250048000 450014183 ApeKI H10 MGP1 H10 zea mays I137TN:C08L7ACXX:6:250048000 +C08L7ACXX 6 CTAGC Va99 MGP1_low_vol A 11 250048001 450014183 ApeKI A11 MGP1 A11 zea mays Va99:C08L7ACXX:6:250048001 +C08L7ACXX 6 GCTCTA IDS28 MGP1_low_vol B 11 250048002 450014183 ApeKI B11 MGP1 B11 zea mays IDS28:C08L7ACXX:6:250048002 +C08L7ACXX 6 GGACCTA W153R MGP1_low_vol C 11 250048003 450014183 ApeKI C11 MGP1 C11 zea mays W153R:C08L7ACXX:6:250048003 +C08L7ACXX 6 CCGGATAT A659 MGP1_low_vol D 11 250048004 450014183 ApeKI D11 MGP1 D11 zea mays A659:C08L7ACXX:6:250048004 +C08L7ACXX 6 TAATA F7 MGP1_low_vol E 11 250048005 450014183 ApeKI E11 MGP1 E11 zea mays F7:C08L7ACXX:6:250048005 +C08L7ACXX 6 GTTGAA EP1 MGP1_low_vol F 11 250048006 450014183 ApeKI F11 MGP1 F11 zea mays EP1:C08L7ACXX:6:250048006 +C08L7ACXX 6 TCGAAGA W182B MGP1_low_vol G 11 250048007 450014183 ApeKI G11 MGP1 G11 zea mays W182B:C08L7ACXX:6:250048007 +C08L7ACXX 6 TATCGGGA CML157Q MGP1_low_vol H 11 250048008 450014183 ApeKI H11 MGP1 H11 zea mays CML157Q:C08L7ACXX:6:250048008 +C08L7ACXX 6 ACAAA A654 MGP1_low_vol A 12 250048009 450014183 ApeKI A12 MGP1 A12 zea mays A654:C08L7ACXX:6:250048009 +C08L7ACXX 6 CCACAA Va22 MGP1_low_vol B 12 250048010 450014183 ApeKI B12 MGP1 B12 zea mays Va22:C08L7ACXX:6:250048010 +C08L7ACXX 6 GTCGATT C103 MGP1_low_vol C 12 250048011 450014183 ApeKI C12 MGP1 C12 zea mays C103:C08L7ACXX:6:250048011 +C08L7ACXX 6 CGCCTTAT H95 MGP1_low_vol D 12 250048012 450014183 ApeKI D12 MGP1 D12 zea mays H95:C08L7ACXX:6:250048012 +C08L7ACXX 6 TACAT CML91 MGP1_low_vol E 12 250048013 450014183 ApeKI E12 MGP1 E12 zea mays CML91:C08L7ACXX:6:250048013 +C08L7ACXX 6 TAACGA CML311 MGP1_low_vol F 12 250048014 450014183 ApeKI F12 MGP1 F12 zea mays CML311:C08L7ACXX:6:250048014 +C08L7ACXX 6 TCTGTGA tripsacum MGP1_low_vol G 12 250048015 450014183 ApeKI G12 MGP1 G12 zea mays tripsacum:C08L7ACXX:6:250048015 +C08L7ACXX 6 TTCCTGGA EMPTY MGP1_low_vol H 12 250048016 450014183 ApeKI H12 MGP1 H12 zea mays EMPTY:C08L7ACXX:6:250048016 diff --git a/COPYING.TXT b/COPYING.TXT new file mode 100644 index 0000000..dba13ed --- /dev/null +++ b/COPYING.TXT @@ -0,0 +1,661 @@ + GNU AFFERO GENERAL PUBLIC LICENSE + Version 3, 19 November 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is 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It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If your software can interact with users remotely through a computer +network, you should also make sure that it provides a way for users to +get its source. For example, if your program is a web application, its +interface could display a "Source" link that leads users to an archive +of the code. There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for the +specific requirements. + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU AGPL, see +. diff --git a/LICENSE b/LICENSE new file mode 120000 index 0000000..ddd512b --- /dev/null +++ b/LICENSE @@ -0,0 +1 @@ +COPYING.TXT \ No newline at end of file diff --git a/README.md b/README.md index 02197cf..9d5486a 100644 --- a/README.md +++ b/README.md @@ -20,6 +20,7 @@ Prerequisites - tassel 3 - bowtie2 - modules +- pandoc Introduction diff --git a/UML/GBS_Discovery_Tassel3_stdTBT.png b/UML/GBS_Discovery_Tassel3_stdTBT.png new file mode 100644 index 0000000..8a99852 Binary files /dev/null and b/UML/GBS_Discovery_Tassel3_stdTBT.png differ diff --git a/UML/GBS_Discovery_Tassel3_stdTBT.txt b/UML/GBS_Discovery_Tassel3_stdTBT.txt new file mode 100644 index 0000000..8fdea96 --- /dev/null +++ b/UML/GBS_Discovery_Tassel3_stdTBT.txt @@ -0,0 +1,189 @@ +@startuml +title GBS Reference Pipeline HapMap and VCF + + +object DirectoryStructure { + GlobalVariables = "Base Path" + LocalVariables = "Dependent on What to run" +} + +object FastqToTagCountPlugin { + GlobalVariables = "Base Path, Tassel Path, MinRam, MaxRam, Keyfile, Enzyme" + LocalVariables = "Plugin Output Path, -s Maximum Good Reads per lane, -c Minimum Tag Count" +} + +object MergeMultipleTagCountPlugin { + GlobalVariables = "Base Path, Tassel Path, MinRam, MaxRam" + LocalVariables = "Plugin Output Path, -o Output File Name, -c Minimum Tag Count" + OptionalVariables = "-t output in fastq text format - if not set outputs in binary cnt format" +} + +object TagCountToFastqPlugin { + GlobalVariables = "Base Path, Tassel Path, MinRam, MaxRam" + LocalVariables = "InputPath, Plugin Output Path, -o Output File Name, -c Minimum Tag Count" +} + +object AlignToGenome { + GlobalVariables = "Base Path, Aligner, Aligner Path, Reference Genome Path" + LocalVariables = "Input Path, Output Path, Aligner flags " +} + +object SAMConverterPlugin { + GlobalVariables = "Base Path, Tassel Path, MinRam, MaxRam" + LocalVariables = "InputPath, Plugin Output Path, -o Output File Name" +} + +object FastqToTBTPlugin { + GlobalVariables = "Base Path, Tassel Path, MinRam, MaxRam, Keyfile Path, TagCountFile Path, Enzyme" + LocalVariables = "InputPath, Plugin Output Path, Output File Name, Upper Bound" +} + +object MergeTagsByTaxaFilesPlugin { + GlobalVariables = "Base Path, Tassel Path, MinRam, MaxRam" + LocalVariables = "InputPath, Plugin Output Path, Output File Name, -s Maximum number of Tags \n-x Merge tag counts of taxa with identical short names --off by default" + Function = "Merge Multiple TBTbyte into 1 TBTbyte" +} + +object TagsToSNPByAlignmentPlugin { + GlobalVariables = "Base Path, Tassel Path, MinRam, MaxRam" + LocalVariables = "InputPath, Plugin Output Path, Output File Name, start chromosome,\n end chromosome, minF, minMAF, minMAC, MinLCov, Include Rare, Include Gaps" +} + + +object MergeDuplicateSNPsPlugin { + GlobalVariables = "Base Path, Tassel Path, MinRam, MaxRam" + LocalVariables = "InputPath, Plugin Output Path, Output File Name, start chromosome, end chromosome" +} + +object GBSHapMapFiltersPlugin { + GlobalVariables = "Base Path, Tassel Path, MinRam, MaxRam" + LocalVariables = "InputPath, Plugin Output Path, Output File Name, \nstart chromosome, end chromosome, MinTaxaCoverage, Min Presence, \nMinF, MNFAF, MXMAF, -mnR2, -mnBonP" +} + +object tbt2vcfPlugin { + GlobalVariables = "Base Path, Tassel Path, MinRam, MaxRam" + LocalVariables = "Input tbt file, Plugin Output Path, start chromosome, end chromosome, \n-ak Maximum number of alleles kept for each marker across pop (default 3), \nMNFAF, Minimum locus coverage" +} + +object MergeDuplicateSNP_vcf_Plugin { + GlobalVariables = "Base Path, Tassel Path, MinRam, MaxRam" + LocalVariables = "Input VCF file, output VCF file, maximum number of alleles kept at each marker location" +} + +object MergeDuplicateTaxa_vcf_Plugin { + GlobalVariables = "Base Path, Tassel Path, MinRam, MaxRam" + LocalVariables = "Input VCF file template, output VCF file template,\n maximum number of alleles kept at each marker location. start chromosome, end chromosome" +} + +object Keyfile { +Bar code / Sample Key +} + +object Fastq.gz { +One or Many +} +object Files { + +Fastq files\n Key File\n Reference Genome +} + +object TagCount { +Tag Count Files +} + +object MasterTagCount { +All tags.\n Minimum Cutoff Set +} + +object TagFastq { +All tags in Fastq Format +} + +object ReferenceGenome { +} + +object Alignment { +SAM formated Alignment +} + +object TOPM { +Tags on Physical Map +} + +object TBTbyte { +Intial TBTbyte File(s) +} + +object MergedTBTbyte { +Merged TBTbyte if needed +} + +object HapMap { +HapMap Files 1 \nper Chromosome +} + +object HapMapMergedSNPs { +Watson and Crick Strand\nidentical SNPs merged +} + +object VCF { +VCF SNP Calls with Dept (max 127) +} + +object VCFMergedSNPs { +Watson and Crick Strand\nidentical SNPs merged +} + +object VCFMergedTaxa { +Identical Taxa Merged\nwhat does identical mean? +} + +DirectoryStructure --|> FastqToTagCountPlugin +FastqToTagCountPlugin --|> MergeMultipleTagCountPlugin +MergeMultipleTagCountPlugin --|> TagCountToFastqPlugin +TagCountToFastqPlugin --|> AlignToGenome +note left of AlignToGenome : Consider a salt in Bowtie2 for reproducability +AlignToGenome --|> SAMConverterPlugin +SAMConverterPlugin --|> FastqToTBTPlugin +FastqToTBTPlugin --|> MergeTagsByTaxaFilesPlugin +MergeTagsByTaxaFilesPlugin --|> TagsToSNPByAlignmentPlugin +tbt2vcfPlugin <|- MergeTagsByTaxaFilesPlugin : Alternate path for SNP calling with VCF output. +TagsToSNPByAlignmentPlugin --|> MergeDuplicateSNPsPlugin +MergeDuplicateSNPsPlugin --|> GBSHapMapFiltersPlugin +tbt2vcfPlugin --|> MergeDuplicateSNP_vcf_Plugin +MergeDuplicateSNP_vcf_Plugin --|> MergeDuplicateTaxa_vcf_Plugin + +Files . DirectoryStructure +DirectoryStructure . Fastq.gz +FastqToTagCountPlugin . TagCount +Fastq.gz ..|> TagCount +Keyfile ..|> TagCount +MergeMultipleTagCountPlugin . MasterTagCount +TagCount ..|> MasterTagCount +TagCountToFastqPlugin . TagFastq +MasterTagCount ..|> TagFastq +AlignToGenome . Alignment +ReferenceGenome .|> Alignment +TagFastq ..|> Alignment +SAMConverterPlugin . TOPM +Alignment ..|> TOPM +FastqToTBTPlugin . TBTbyte +Fastq.gz ..|> TBTbyte +MasterTagCount ..|> TBTbyte +Keyfile ..|> TBTbyte +MergeTagsByTaxaFilesPlugin . MergedTBTbyte +TBTbyte ..|> MergedTBTbyte +MergeDuplicateSNPsPlugin . HapMapMergedSNPs + +TagsToSNPByAlignmentPlugin . HapMap +TOPM ..|> HapMap +MergedTBTbyte ..|> HapMap +HapMap ..|> HapMapMergedSNPs +tbt2vcfPlugin .. VCF +TOPM ..|> VCF +MergedTBTbyte ..|> VCF +VCF ..|> VCFMergedSNPs +MergeDuplicateSNP_vcf_Plugin . VCFMergedSNPs +VCFMergedSNPs ..|> VCFMergedTaxa +MergeDuplicateTaxa_vcf_Plugin . VCFMergedTaxa +@enduml \ No newline at end of file diff --git a/UML/README.md b/UML/README.md new file mode 100644 index 0000000..985500b --- /dev/null +++ b/UML/README.md @@ -0,0 +1,3 @@ + +# Plugin UML Diagrams +The files in this directory are UML text and corresponding PNG images. They are meant to show the relationship of TASSEL3 plugins and files. diff --git a/doc/images/SnipImage_SNPCaller.jpg b/doc/images/SnipImage_SNPCaller.jpg new file mode 100644 index 0000000..06b3edc Binary files /dev/null and b/doc/images/SnipImage_SNPCaller.jpg differ diff --git a/doc/images/SnipImage_genotypes.jpg b/doc/images/SnipImage_genotypes.jpg new file mode 100644 index 0000000..08e07db Binary files /dev/null and b/doc/images/SnipImage_genotypes.jpg differ diff --git a/doc/images/SnipImage_tagsByTaxa.jpg b/doc/images/SnipImage_tagsByTaxa.jpg new file mode 100644 index 0000000..b17d597 Binary files /dev/null and b/doc/images/SnipImage_tagsByTaxa.jpg differ diff --git a/doc/images/flowDiagram.jpg b/doc/images/flowDiagram.jpg new file mode 100644 index 0000000..4fde853 Binary files /dev/null and b/doc/images/flowDiagram.jpg differ diff --git a/doc/images/flowDiagram_tagCounts.jpg b/doc/images/flowDiagram_tagCounts.jpg new file mode 100644 index 0000000..5794b04 Binary files /dev/null and b/doc/images/flowDiagram_tagCounts.jpg differ diff --git a/doc/images/flowDiagram_topm.jpg b/doc/images/flowDiagram_topm.jpg new file mode 100644 index 0000000..0e90cbb Binary files /dev/null and b/doc/images/flowDiagram_topm.jpg differ diff --git a/run_all.R b/run_all.R new file mode 100644 index 0000000..77fd74e --- /dev/null +++ b/run_all.R @@ -0,0 +1,12 @@ +library(knitr) + +knit("00_AlignerIndices/run.Rmd") +knit("01_RawSequence/run.Rmd") +knit("02_TagCounts/01_IndividualTagCounts/run.Rmd") +knit("02_TagCounts/02_MergedTagCounts/run.Rmd") +knit("02_TagCounts/03_TagCountToFastq/run.Rmd") +knit("03_SAM/run.Rmd") +knit("04_TOPM/run.Rmd") +knit("05_TBT/01_IndividualTBT/run.Rmd") +knit("05_TBT/04_PivotMergedTaxaTBT/run.Rmd") +knit("06_HapMap/run.Rmd") diff --git a/test/test.Rmd b/test/test.Rmd index e9ea9df..be2843e 100644 --- a/test/test.Rmd +++ b/test/test.Rmd @@ -2,10 +2,18 @@ ```{r test-bash, engine='bash'} -wget -h +R --version +RScript -e "library(knitr);" +wget --version +unzip --version +wget --version unzip -h bowtie2 -h run_pipeline.pl -h +pandoc --version +module --version + + pandoc test.md -o test.html