New Varient Calling Tools/Consider GATK #37
I was thinking why we are using bcftools to call SNVs. I have not used bcftools extensively. It is a genotyper caller the same as UnifiedGenotyper in GATK? for somatic mutations, I have used GATK (mutect1) recently, but it requires a lot of work to get a workable bam file: indel-realignment(mutect2 can skip this step but not stable yet), base quality recab etc... In a real world task with human genome, GATK is very slow, I have to parallelize every step by chromosome.
am working on a Snakemake pipeline on it for my own use: https://gitlab.com/tangming2005/snakemake_DNAseq_pipeline/tree/freebayes_anno
@JasonJWilliamsNY - Since we're preparing to release at the end of this month, I propose we hold off on any major content changes until our next release. Would love to have more discussion from the community on this issue to decide whether it's a good idea to make this change for then.