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broadinstitute / gatk

Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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Merging phased indels #6460

Open asgerjakobsen opened 4 years ago

asgerjakobsen commented 4 years ago

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?

droazen commented 4 years ago

@davidbenjamin ^^

lvzenglei commented 2 weeks ago

Any Solutions? Thanks~