Deletion is split into two deletions
Answered
If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 4.2.0.0
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.
Best regards
Maximilian Dörrbecker
PS: The link to the BAM, BAM.BAI and VCF file is:
https://jlubox.uni-giessen.de/dl/fiWnqkJuUj5wf9kggP3HGs7v/.zip
If you need anything else, please let me know.
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Thanks for writing into the forum with this question! In determining why a certain haplotype is called, I would recommend to first take a look at this article and walk through the troubleshooting steps: When HaplotypeCaller and Mutect2 do not call an expected variant. It was written by our developers to better understand and troubleshoot tricky calls.
Let me know if you have further questions after taking a look.
Best,
Genevieve
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