generate multi-sample vcf metrics for release

Kurt-Hetrick / CIDR_SEQ_CAPTURE_JOINT_CALL

CIDR exome and targeted resequencing joint calling/filtering pipeline

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Closed Kurt-Hetrick closed 2 years ago

Kurt-Hetrick commented 4 years ago

total number of SNVs on Bait: count of pass snv sites in vcf: need to generate sub-site vcf and count then delete.

total number of indels on Bait: count of pass mixed + indel sites in vcf: need to generate sub-site vcf and count then delete.

Kurt-Hetrick commented 4 years ago

can use variant summary stat files for this

Kurt-Hetrick commented 4 years ago

add to completion summary. in addition to myself and teams send to cidr sequencing notifications.

Kurt-Hetrick commented 2 years ago

integrated into STD_VQSR. will port over to other pipelines in the future.