GATK

This category contains 14 nodes.

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

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

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

Recalibration of sequencing quality scores.

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

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

Realignment around insertions and deletions.

Selects a subset of variants from a larger callset.

Calls SNPs and indels.

Filters variant calls based on INFO and FORMAT annotations.