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insertions like AAAAAA/GGGGGG/CCCCCC/TTTTTT by Mutect2
I recently got a very frustrated result by GATK4.0 Mutect2 for some of my tumor samples. They dumped out too many insertions like AAAAAA / GGGGGG / CCCCCC / TTTTTT which seem to mostly be artifacts. VAFs are generally low but determined as significant ones at the final step and even many of them are located in exonic regions. I got lost at this point so just want to hear any experience or possible explanations?
- again, this is happening only in subset of samples that went through the same pipeline together. Also, I don't see any noticeable insertions when manually taking a look at original BAM files for each location.
This is showing an example of paired reads in bamout (upper pannel) and the original BAM file (bottom one). The dark read ones are the same read bearing 'AAAAAA' insertion in one of the pairs.