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Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
Perl C++ C Other
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README.md

Setup

docker

git clone https://github.com/aquaskyline/16GT.git
cd 16GT
docker build --no-cache .
docker images

use the respective "IMAGE ID" displayed above as below

docker run -it --privileged <docker-id> /bin/bash

once inside the docker image, index the reference

cd /16GT/SOAP3-dp
./soap3-dp-builder <path-to-ref-gen-fasta>
./BGS-Build <path-to-ref-gen-fasta>.index

variant call using aligned/indexed bam file

cd /16GT
./bam2snapshot -i <path-to-ref-gen-fasta>.index -b <aligned-bam-file> -o <output-prefix>
./snapshotSnpcaller  -i <path-to-ref-gen-fasta>.index  -o <output-prefix>
perl txt2vcf.pl <output-prefix>.txt <pro-id> <path-to-ref-gen-fasta> > <output>.vcf
perl filterVCF.pl <output>.vcf > <output>.filtered.vcf

16GT

16GT is a variant caller utilizing a 16-genotype probabilistic model to unify SNP and indel calling in a single algorithm. 16GT is easy to use. The default parameters will fit most of the use cases with human genome. For the detailed parameters for each module, please run the module to get an info.

Quick start

Inputs: genome.fa alignments.bam, Output: .vcf

0. Install

git clone https://github.com/aquaskyline/16GT
cd 16GT
make
# Tested in Ubuntu 14.04 and CentOS 6.7 with GCC 4.7.2

1. Build reference index

git clone https://github.com/aquaskyline/SOAP3-dp.git
cd SOAP3-dp
make SOAP3-Builder
make BGS-Build
soap3-dp-builder genome.fa
BGS-Build genome.fa.index

2. Convert BAM to SNAPSHOT

bam2snapshot -i genome.fa.index -b alignments.bam -o output/prefix

3. Call

snapshotSnpcaller -i genome.fa.index -o output/prefix
perl txt2vcf.pl output/prefix.txt sampleName genome.fa > <output>.vcf
perl filterVCF.pl <output>.vcf dbSNP.vcf.gz > <output>.filtered.vcf

Exome variant calling

Inputs: genome.fa alignement.bam region.bed, Outputs: region.bin .vcf

RegionIndexBuilder genome.fa.index region.bed region.bin -bed/-gff
bam2snapshot -i genome.fa.index -b alignments.bam -o output/prefix -e region.bin
snapshotSnpcaller -i genome.fa.index -o output/prefix -e region.bin

License

GPLv3

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