If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 126.96.36.199
b) Exact command used:
gatk Mutect2 -I extracted.bam -R hg19_reference.fasta -O extracted_called_variants.vcf
c) Entire error log: No error.
If not an error, choose a category for your question(REQUIRED):
I prepared a test case for my scenario. In my BAM file there is a deletion of 15bps with an adjacent SNP detected in multiple reads. I could also verify this in the IGV browser and also in the BAMs CIGAR String and MD:Z & MC:Z Flag.
So next up, I called variants with Mutect2 for this region and it does split the 15bp deletion into two deletions as you could see in the attached VCF file.
As I couldn't find any clue about such an interaction, I would like you to look over this and maybe help me with this problem.
PS: The link to the BAM, BAM.BAI and VCF file is:
If you need anything else, please let me know.
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