svtyper

Bayesian genotyper for structural variants

Example workflow

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

Genotype with SVTyper

zcat NA12878.20.vcf.gz \
    | ./svtyper \
        -B NA12878.20.bam \
        -S NA12878.20.splitters.bam \
        > NA12878.20.gt.vcf

Warning

2015-10-05

As of 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.