Hi GATK Team,
I wonder if there is any indication in the outputs / intermediate files for regions that triggered M2 realignment if I did not use -bamout in M2?
My another question is, what should be the input bam for FilterAlignmentArtifact? I saw "The bam input to this tool should be the reassembly bamout produced by HaplotypeCaller or Mutect2 in the process of generating the input callset. " in the document (https://gatk.broadinstitute.org/hc/en-us/articles/360037226112-FilterAlignmentArtifacts-EXPERIMENTAL-), however in best-pratice WDL, I saw the input bam is tumor bam. (https://github.com/gatk-workflows/gatk4-somatic-snvs-indels/blob/master/mutect2.wdl#L361). Could you please clarify?
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