GATK Joint Genotyping#

23/03/2022

For germline short variants (SNPs and indels), the GATK workflow includes a joint analysis step that empowers variant discovery by providing the ability to leverage population-wide information from a cohort of multiple samples, allowing us to detect variants with great sensitivity and genotype samples as accurately as possible. Atgenomix demonstrates the power of the SeqsLab platform in this case study by executing the GATK Joint Genotyping pipeline, which is based on the Github Project, JointGenotyping_v1.5.1 (external link).

Main WDL#

The main WDL used in this example can be referenced from the Atgenomix public GitHub account (external link).

WOM graph#

WOM Graph of main wdl

Performance Evaluation#

Performance (Time)

52 samples

60 samples

CheckSamplesUnique

3m:50s

SplitIntervalList

26s

ImportGVCFs

24m:31s

GenotypeGVCFs

12m:25s

HardFilterAndMakeSitesOnlyVcf

1m:31s

SitesOnlyGatherVcf

2m:33s

IndelsVariantRecalibrator

54m:20s

SNPsVariantRecalibratorClassic

1h:18m:45s

ApplyRecalibration

2m:19s

CrossCheckFingerprintSolo

5h:23m:00s

FinalGatherVcf

9m:56s

CollectMetricsOnFullVcf

1h:11m:49s

Total

7h:43m:21s