Recently I run Gatk-Mutect2 to call the somatic mutations in my data, but I get a lot more (too much and seems abnormal) mutations than I expected. I supposed that there should be some filter I need to do to filter out those germline mutations. But I am not quite sure what filters should I do. Is there a column that contains information of germline or somatic? Or is there any steps I should run?
I only run Mutect2 (input:bam) to get my result.
•
written
by
Laven9 •
1 answer
It seems like you ran tumor-only mode of Mutect2. Did you only put tumor bam file as an input?
Mutect2 needs 2 bam files for accurate mutation calling: tumor and its matching normal.
If you just use a tumor bam file, it will also call false positives which may lead to larger number of somatic mutations.
You could refer https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php
for the other command options.
Log in to answer this question.
-
How to calculate tumor mutation burden (TMB)?
written by tanbiswas6 •
-
Get both somatic and germline mutations from tumor only sample?
written by wormball •
-
Are there any repository for panel of normal for running Mutect2?
written by DareDevil
-
Somatic variant calling mutect2 tumour only
written by cellulebioinfobiscem •
-
Mutation calling for pediatric cancer data
written by Gene_MMP8
-
GATK4 (4.1.2.0) Mutect2 --germline-resource option
written by romagnoli.simone •
-
Filtering significant somatic variants from a VCF file
written by gprashant17
-
the difference between the positions called by somatic caller (MuTect2) and the position called by …
written by Zoey Zou •
-
Mutect2 "somatic" variants with resistant tissue culture lines
written by shawn.w.foley
-
Variant calling on single sample Macaque WGS data - advice please
written by BioinfGuru
