merge v0.1.0

.travis.yml

@@ -22,6 +22,7 @@ install:
 
 script:
     - cd test && ./test.sh
+    - python test_svtyper.py
 
 # # command to install dependencies
 # install:

README.md

@@ -1,30 +1,68 @@
-svtyper
+SVTyper
 =======
 [![GitHub license](https://img.shields.io/badge/license-MIT-blue.svg)](https://raw.githubusercontent.com/hall-lab/svtyper/master/LICENSE)
 [![Build Status](https://travis-ci.org/hall-lab/svtyper.svg?branch=master)](https://travis-ci.org/hall-lab/svtyper)
 
 Bayesian genotyper for structural variants
 
-### Example workflow
+## Example
 
-#### Data
 ```
-wget http://colbychiang.com/hall/cshl_sv_2014/data/NA12878.20.bam
-wget http://colbychiang.com/hall/cshl_sv_2014/data/NA12878.20.bam.bai
-wget http://colbychiang.com/hall/cshl_sv_2014/data/NA12878.20.splitters.bam
-wget http://colbychiang.com/hall/cshl_sv_2014/data/NA12878.20.splitters.bam.bai
-wget http://colbychiang.com/hall/cshl_sv_2014/data/NA12878.20.vcf.gz
+svtyper \
+    -i sv.vcf \
+    -B sample.bam \
+    -l sample.bam.json \
+    > sv.gt.vcf
 ```
 
-#### Genotype with SVTyper
+## Overview
+
+SVTyper performs breakpoint genotyping of structural variants (SVs) using whole genome sequencing data. Users must supply a VCF file of sites to genotype (which may be generated by [LUMPY](https://github.com/arq5x/lumpy-sv)) as well as a BAM/CRAM file of Illumina paired-end reads aligned with [BWA-MEM](https://github.com/lh3/bwa). SVTyper assesses discordant and concordant reads from paired-end and split-read alignments to infer genotypes at each site. Algorithm details and benchmarking are described in [Chiang et al., 2015](http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3505.html).
+
+![NA12878 heterozygous deletion](etc/het.png?raw=true "NA12878 heterozygous deletion")
+
+## Installation
+
+Requirements
+- Python 2.7 or newer
+- Pysam 0.8.1 or newer
+
+Clone the repository
+```
+git clone git@github.com:hall-lab/svtyper.git
+```
+
+Test the installation
+```
+cd svtyper/test
+
+../svtyper \
+    -i example.vcf \
+    -B NA12878.target_loci.sorted.bam \
+    -l NA12878.bam.json
+    > test.vcf
 ```
-zcat NA12878.20.vcf.gz \
-    | ./svtyper \
-        -B NA12878.20.bam \
-        -S NA12878.20.splitters.bam \
-        > NA12878.20.gt.vcf
+
+## Troubleshooting
+
+Many common issues are related to abnormal insert size distributions in the BAM file. SVTyper provides methods to assess and visualize the characteristics of sequencing libraries.
+
+Running SVTyper with the `-l` flag creates a JSON file with essential metrics on a BAM file. SVTyper will sample the first N reads for the file (1 million by default) to parse the libraries, read groups, and insert size histograms. This can be done in the absence of a VCF file.
+```
+svtyper \
+    -B my.bam \
+    -l my.bam.json
+```
+
+The [lib_stats.R](scripts/lib_stats.R) script produces insert size histograms from the JSON file
+```
+scripts/lib_stats.R my.bam.json my.bam.json.pdf
 ```
-#### Warning
-2015-10-05
+![Insert size histogram](etc/my.bam.json.png?raw=true "Insert size histogram")
+
+
+## Citation
+
+C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Marth, A R Quinlan, and I M Hall. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Meth 12, 966–968 (2015). doi:10.1038/nmeth.3505.
 
-As of commit [2c2ef7f91698a6d2929430f0865402ad421a8e3d](https://github.com/hall-lab/svtyper/commit/2c2ef7f91698a6d2929430f0865402ad421a8e3d), SVTyper assumes that BAMs were aligned with BWA MEM **without** the "-M" flag. If you used the "-M" flag in your alignment, then you should also use the "-M" flag when running SVTyper.
+http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3505.html