Objective
After variant calling on chrM, filter the calls with FilterMutectCalls so unreliable variants might be filtered out (this step is also part of GATK best practices).
Proposed demo
Maybe show number of variants in vcf before and after implementing filtermutect and also which kind of calls are removed (calls with HL <0.01 for example?)
Proposed requirements
Branch feat/implement_gatk_mtdna_snv_calling is done, accepted and merged (?)
Implementation suggestion (optional)
Add this step after variant calling and before vcf merging. Take inspiration from mtDNA-Server 2
Additional context (optional)
This step is part of GATK best practices guidelines
Objective
After variant calling on chrM, filter the calls with FilterMutectCalls so unreliable variants might be filtered out (this step is also part of GATK best practices).
Proposed demo
Maybe show number of variants in vcf before and after implementing filtermutect and also which kind of calls are removed (calls with HL <0.01 for example?)
Proposed requirements
Branch
feat/implement_gatk_mtdna_snv_callingis done, accepted and merged (?)Implementation suggestion (optional)
Add this step after variant calling and before vcf merging. Take inspiration from mtDNA-Server 2
Additional context (optional)
This step is part of GATK best practices guidelines