Update README.md

README.md

@@ -15,13 +15,75 @@ curl -sL mutserve.vercel.app | bash
 ```
 
 ## Documentation
-Full documentation for mutserve can be found [here](https://mitoverse.readthedocs.io/mutserve/mutserve/). 
+
+### Quick Start
+Mutserve requires sorted and indexed CRAM/BAM files as an input.
+
+```
+curl -sL mutserve.vercel.app | bash
+./mutserve
+```
+
+### Available Tools
+Currently two tools are available. 
+
+* **call**: Variant Calling of homoplasmic and heteroplasmic positions. 
+* **annotate**:  Annotation of mutserve variants (generated with `mutserve call`). 
+
+### Mutserve Variant Calling
+
+```
+wget https://github.com/seppinho/mutserve/raw/master/test-data/mtdna/bam/input/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
+curl -sL mutserve.vercel.app | bash
+./mutserve call --reference rCRS.fasta --output HG00096.vcf.gz --threads 4 *.bam 
+```
+
+Please use [this reference file](https://raw.githubusercontent.com/seppinho/mutserve/master/files/rCRS.fasta) when using BAQ (disabled by default since v2.0.0).
+
+### Mutserve Annotation
+
+Mutserve allows to annotate the variant file (.txt) with a predefined [annotation file](https://raw.githubusercontent.com/seppinho/mutserve/master/files/rCRS_annotation_2020-08-20.txt) 
+
+```
+./mutserve annotate --input variantfile.txt --annotation rCRS_annotation_2020-08-20.txt --output AnnotatedVariants.txt
+```
+
+### Parameters
+
+| Parameter        | Default Value / Comment          | Command Line Option | 
+| ------------- |:-------------:| :-------------:| 
+| Input Files     | sorted and indexed BAM/CRAM files | |
+| Output Name   | output file; supported: \*.txt, \*.vcf, \*vcf.gz | `--output` |
+| Reference  | reference file | `--reference` |
+| Threads     | 1 | `--threads`|
+| Minimum Heteroplasmy Level     | 0.01 | `--level`|
+| Define specific mtDNA contig in whole-genome file     | null | `--contig-name`|
+| Output Fasta     | false | `--writeFasta`|
+| Output Raw File     | false | `--writeRaw`|
+| MappingQuality     | 20 | `--mapQ`|
+| BaseQuality     | 20 | `--baseQ`|
+| AlignmentQuality     | 30 | `--alignQ`|
+| Enable Base Alignment Quality (BAQ)     | false | `--baq`|
+| Disale 1000 Genomes Frequence File     | false | `--noFreq`|
+| Call deletions (beta)     | false | `--deletions`|
+| Call insertions (beta)     | false | `--insertions`|
+| Disable ANSI output     |  | `--no-ansi`|
+| Show version     |  | `--version`|
+| Show help     |  | `--help`|
+
+## Output Formats
+
+### Tab delimited File
+By default (`--output filename` does not end with .vcf or .vcf.gz) we export a TAB-delimited file including *ID, Position, Reference, Variant & VariantLevel*. Please note that the *VariantLevel* always reports the non-reference variant level. The output file also includes the **most** and **second most base** at a specific position (MajorBase + MajorLevel, MinorBase+MinorLevel). The reported variant can be the major or the 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. 
+
+### VCF
+If you want a **VCF** file as an output, please specify `--output filename.vcf.gz`. Heteroplasmies are coded as 1/0 genotypes, the heteroplasmy level is included in the FORMAT using the **AF** attribute (allele frequency) of the first non-reference allele. Please note that indels are currently not included in the VCF.  This VCF file can be used as an input for https://github.com/seppinho/haplogrep-cmd.
 
 ## Limitations
-The focus of mutserve is currenly on SNP calling and not on indels.
+The focus of mutserve is currenly on SNP calling and not on indels. Please checkout [mtDNA-Server 2](https://github.com/genepi/mtdna-server-2/) to combine SNV with InDel Calling. 
 
 ## Contact
-See [here](https://mitoverse.readthedocs.io/contact/).
+[Sebastian Schoenherr](mailto:[email protected])
 
 ## Citation