GATK

This category contains 14 nodes.

CombineGVCFs 

Combines any number of gVCF files that were produced by the Haplotype Caller into a single joint gVCF file.

CombineVCFs 

Combines any number of VCF lists that were produced by Pindel into a single joint VCF file.

DepthOfCoverage 

Assess sequence coverage by a wide array of metrics, partitioned by sample, read group, or library.

GATKBaseRecalibration 

Recalibration of sequencing quality scores.

GATKHaplotypeCaller 

Calls germline SNPs and indels via local re-assembly of haplotypes.

GATKPhaseByTransmission 

Computes the most likely genotype combination and phases trios and parent/child pairs.

GATKRealignment 

Realignment around insertions and deletions.

GATKSelectVariants 

Selects a subset of variants from a larger callset.

GATKUnifiedGenotyper 

Calls SNPs and indels.

GATKVariantFiltration 

Filters variant calls based on INFO and FORMAT annotations.