Merge branch 'master' of https://github.com/seppinho/mutation-server.git

README.md

@@ -15,6 +15,9 @@ wget https://github.com/seppinho/mutation-server/releases/download/v1.1.5/mutati
 java -jar mutation-server-1.1.5.jar  analyse-local --input <input-folder> --reference <ref.fasta> --level 0.01 --outputRaw raw.txt --outputVar var.txt --baq true --baseQ 20 --mapQ 20 --alignQ 30 --indel true
 ```
 
+## Output Format
+We report variants in a TAB delimited file including *SampleID, Position, Reference, Variant & Variant-Level*. Please not that the Variant-Level is always the non-reference level. We also include the the **most** and **second most base** at a specific position (so called Major/Minor Component). The last column includes the type of the variant (1: Homoplasmy, 2: Heteroplasmy or Low-Level Variant, 3: Low-Level Deletion, 4: Deletion, 5: Insertion). See [here](https://raw.githubusercontent.com/seppinho/mutation-server/master/test-data/results/variantsLocal1000G) for an example. 
+
 ## Citation
 If you use this tool, please cite [this paper](http://nar.oxfordjournals.org/content/early/2016/04/15/nar.gkw247.full).
 

test-data/results/README.txt

@@ -0,0 +1 @@
+

test-data/results/variantsLocal1000G

@@ -0,0 +1,24 @@
+SampleID	Pos	Ref	Variant	Variant-Level	Major/Minor	Major-Percentage/Minor-Percentage	Coverage-Total
+HG00096_mapped_ILLUMINA_bwa_GBR_low_coverage_20101123	10394	C	T	0.999	T/-	0.999/0.001	1455	1
+HG00096_mapped_ILLUMINA_bwa_GBR_low_coverage_20101123	12410	A	G	0.011	A/G	0.989/0.011	1489	2
+HG00096_mapped_ILLUMINA_bwa_GBR_low_coverage_20101123	14071	A	G	0.011	A/G	0.989/0.011	1672	2
+HG00096_mapped_ILLUMINA_bwa_GBR_low_coverage_20101123	1438	A	G	1.00	G/-	1.00/0.00	1246	1
+HG00096_mapped_ILLUMINA_bwa_GBR_low_coverage_20101123	1456	T	C	0.01	T/C	0.988/0.01	1285	2
+HG00096_mapped_ILLUMINA_bwa_GBR_low_coverage_20101123	14569	G	A	0.575	A/G	0.575/0.424	1555	2
+HG00096_mapped_ILLUMINA_bwa_GBR_low_coverage_20101123	152	T	C	0.999	C/-	0.999/0.001	1379	1
+HG00096_mapped_ILLUMINA_bwa_GBR_low_coverage_20101123	15326	A	G	0.999	G/-	0.999/0.001	1315	1
+HG00096_mapped_ILLUMINA_bwa_GBR_low_coverage_20101123	15340	A	G	1.00	G/-	1.00/0.00	1349	1
+HG00096_mapped_ILLUMINA_bwa_GBR_low_coverage_20101123	15463	A	G	0.013	A/G	0.988/0.013	1120	2
+HG00096_mapped_ILLUMINA_bwa_GBR_low_coverage_20101123	16093	T	C	0.595	C/T	0.595/0.404	1407	2
+HG00096_mapped_ILLUMINA_bwa_GBR_low_coverage_20101123	16360	C	T	0.386	C/T	0.614/0.386	1224	2
+HG00096_mapped_ILLUMINA_bwa_GBR_low_coverage_20101123	16519	T	C	0.999	C/-	0.999/0.001	838	1
+HG00096_mapped_ILLUMINA_bwa_GBR_low_coverage_20101123	263	A	G	1.00	G/-	1.00/0.00	1137	1
+HG00096_mapped_ILLUMINA_bwa_GBR_low_coverage_20101123	2746	T	C	0.025	T/C	0.975/0.025	1378	2
+HG00096_mapped_ILLUMINA_bwa_GBR_low_coverage_20101123	303.1	-	C	1.00	C/-	1.00/0.00	404	5
+HG00096_mapped_ILLUMINA_bwa_GBR_low_coverage_20101123	3107	N	D	0.97	D/T	0.97/0.024	1231	4
+HG00096_mapped_ILLUMINA_bwa_GBR_low_coverage_20101123	311.1	-	C	1.00	C/-	1.00/0.00	401	5
+HG00096_mapped_ILLUMINA_bwa_GBR_low_coverage_20101123	3200	T	C	0.01	T/C	0.99/0.01	1468	2
+HG00096_mapped_ILLUMINA_bwa_GBR_low_coverage_20101123	4769	A	G	1.00	G/-	1.00/0.00	704	1
+HG00096_mapped_ILLUMINA_bwa_GBR_low_coverage_20101123	750	A	G	1.00	G/-	1.00/0.00	910	1
+HG00096_mapped_ILLUMINA_bwa_GBR_low_coverage_20101123	8592	G	A	1.00	A/-	1.00/0.00	1578	1
+HG00096_mapped_ILLUMINA_bwa_GBR_low_coverage_20101123	8860	A	G	0.996	G/-	0.996/0.004	270	1