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Published 20 hours ago • verified publisher icon broadinstitute

Merging phased indels

Open asgerjakobsen opened this issue 5 years ago • 2 comments

We are performing somatic variant calling in tumour-only mode where we call variants with both Mutect2 (GATK version 4.1.2.0) and Vardict-java. We have noticed that Mutect2 calls adjacent phased indels as two separate variants, whereas Vardict calls these as a single variant. We have tried increasing the value of the --max-mnp-distance option, and this merges SNP-SNP combinations into an MNP but does not merge phased combinations of INDEL-SNP or INDEL-INDEL. Is there any way this could be implemented?

asgerjakobsen avatar Feb 19 '20 17:02 asgerjakobsen