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# Mutect2 dont list Variant

KielMember

Hi,
Iam running mutect2 on capture data, with tumor normal. The data flows the "classic" way on a local wdl-pipeline with bwa =>merge=>markDup=>recal=>mutect2 (3.6).

I see the variant clearly in IGV in both tumor and normal sample and even in the bamout i created for it (see screenshot). But it dont get listed in the output vcf.

I know that mutect2 apply some hard filters to the variant, but I should see the variant in the output marked with an alt_allele_in_normal ?

Greetings

=>tumot
=>normal
=>bamout

Tagged:

I see the variant clearly in IGV in both tumor and normal sample

MuTect2 is a somatic caller that only calls on differences in the tumor from the normal. However, as you say, the call should be present with an annotation that filters it. Your screenshots, are these the raw BAMs or the BAMOUTs from a MuTect2 run?

• KielMember

Hi @shlee,
thank you for you answer...the screenshots are showing in order tumor.raw.bam, normal.raw.bam and tumor-normal.bamout.bam.

The BAMOUT needs to by grouped by sample, colored by HC tag and sorted by HC tag. Also, can you show the reference sequence and genomic location for this locus? You've previously done a helpful IGV coloring at the end of this thread for a MuTect2 BAMOUT.

In general, we need more information than what you've so far provided to effectively answer questions such as why a variant wasn't called. Please help us help you more effectively by provided the needed information up front so we can minimize this back and forth. We are a small team. Thanks.

• KielMember

@shlee
sry:(...i made a new screenshot and hope it will satisfy and also I will provide some helpful information (hope so .
I run the pipline in the broadinstitute/genomes-in-the-cloud 2.2.4-1469632282 Docker container with cromwell version 21, so its gatk 3.6.
Furthermore i use scatter/ghatter and merging the resulting vcf´s. My command for mutect2 is:

    java -Xmx4g -jar /usr/gitc/GATK36.jar \
-T MuTect2 \
--dbsnp ${dbSNP_vcf} \ -dt NONE \ -R${ref_fasta} \
-I:normal ${input_normal_bam} \ -I:tumor${input_tumor_bam} \
-L ${interval_list} \ -o${vcf_basename}.MT.vcf
`

#### Issue · Github February 17 by shlee

Issue Number
1748
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
sooheelee

Thanks for supplying a better screenshot. I hope there is an easy explanation for this odd phenomena @EADG. Would you mind generating a snippet of the data needed to recreate this image, i.e. your tumor and normal raw BAMs as well as your BAMOUT and callset? Instructions for sending us data are at http://gatkforums.broadinstitute.org/gatk/discussion/1894/how-do-i-submit-a-detailed-bug-report.

• KielMember

Hi @shlee

i manage to upload the Files to your server (gosh that 20 user limitation is quite an annoyance). The Folder is EADG-Mutect2.

I have observe the same issue with an other sample which carries the same variant...Do you mean i it is useful when I check if i get the variant called with HC, since the relationship between HC and Mutect2 ?

Thank you!

• KielMember

Hi @shlee,

just to be shure I checked the position an noticed that all of them have rs-numbers and are included in dbSNP. I know you have plenty off other stuff to do...argh but you have a little status update for me ?

@Sheila has returned from her conference and she should be able to help you going forward, especially given your question requires in-depth probing. I've just been filling in for the team this last week since most are away.

Hi,

I will have a look and get back to you soon.

-Sheila

As I recall M2 doesn't call obvious germline variants, or at least it's not supposed to, no? My impression was that we only output "germline_risk" records if they have a chance of being somatic and are borderline. If they're obviously germline, why bother? Would just make much bigger files for nothing... But I may have misunderstood the default behavior.
• KielMember

Hi everbody and thank for your effort,
if its like @Geraldine_VdAuwera said it is ok, but I need an "official" confirm, because I find nothing about it in the doc´s.
Maybe a verbose-mode were good were mutect2 puts every think out even it is a obviously germline variant. Just to be shure everything is allright.

Thanks so far!