Tool Reference

Category

Tool

Variant Calling

• deepvariant_germline

• deepvariant

• germline (GATK Germline Pipeline)

• haplotypecaller

• postpon

• prepon

• somatic (Somatic Variant Caller)

• mutectcaller

Quality Control

• bammetrics

• collectmultiplemetrics

GVCF Processing

• indexgvcf

• genotypegvcf