Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
MNP calling problem in GATK4 Mutect2 beta
I tried to use GATK4 Mutect2 to call somatic mutations and found some weird MNP results:
CHROM POS REF ALT
chr2 157214886 GT TT
chr4 130772884 CGTGT TGTGT
chr4 145617203 TAAA AAAA
chr5 7857891 CAA AAA
chr5 30904821 AT TT
It sounds these variants should be simple SNPs however called as MNP here. Is it a bug in variant calling of Mutect2? Does GATK4 Mutect2 support MNP calling now?