Open chandrans opened 7 years ago
@chandrans HaplotypeCaller
(even in GATK3) can't usually call large indels. Does GATK3 HaplotypeCaller
make this call?
I'll also add: GATK4's HaplotypeCaller
is beta, and not yet ready for production use. It does not currently match the output of the GATK3 HaplotypeCaller
.
Hi David. This was not called in GATK3 either. It is more a question of whether this should be called by HC because the user says it is a verified indel. We should be calling verified true indels. The user says it is 50bp, and HC has called things larger than that before.
I am not sure if this is a bug, but more asking if this is a potential CNV from the looks of the coverage? Or, what kind of args the user can provide to get the "indel" called?
Bug Report
Affected tool(s)
HaplotypeCaller
Affected version(s)
latest GATK4
Description
A user reported a verified 50 bp insertion is not being called with HaplotypeCaller. On closer inspection, I noticed the coverage is really odd in the region. Original BAM:
bamout:
Steps to reproduce
The files are here:
/humgen/gsa-scr1/schandra/asaki_InsertionNotCalled
Command: `./gatk-launch HaplotypeCaller -R human_g1k_v37.fasta -I GW
I127.rs1799752.bam -O Sheila.HaplotypeCaller.vcf -bamout Sheila.HaplotypeCaller.bam`
Expected behavior
Is this insertion supposed to be called? Need clarification from Methods.
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