16GT

16GT is a variant caller utilizing a 16-genotype probabilistic model to unify SNP and indel calling in a single algorithm.

Quick start

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

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

Exome variant calling

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