Why are full regions removed in the bamout file of Mutect2 when compared to the input files?
Dear GATK Team,
As referred to in a separate post, in the (Notebook) Intro to using Mutect2 for somatic data documentation, there are two IGV images in the section 'REVIEW CALLS WITH IGV', and the TP53 locus at chr17:7,666,402-7,689,550 is being assessed.
Regarding the IGV image focusing on the above locus in tumor.bam and normal.bam (input files) and 2_tumor_normal_m2.bam (bamout file), there are regions with coverage in tumor.bam and normal.bam but with no coverage at all in 2_tumor_normal_m2.bam. Is this due to regions being excluded in the step that defines ActiveRegions or another step? Are reasons for regions being excluded multifactorial or due to one predominant reason?
Thank you for your time and help.
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The bamout only contains regions where local assembly occurred due to the possiblity of somatic variation.
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