Versions of tools in order of process
Tool
Version
FastqToBam (Fgbio)
1.2.0
SamToFastq (Picard tools part of GATK)
4.1.8.0
0.20.1
4.1.8.0
0.7.17
AddOrReplaceReadGroups (Picard tools part of GATK)
4.1.8.1
MergeBamAlignment (Picard tools part of GATK)
4.1.8.0
MarkDuplicates (Picard tools part of GATK)
4.1.8.1
GenomeCov (Bedtools)
2.28.0_cv2
Merge (Bedtools)
2.28.0_cv2
2.22
FixMateInformation (Picard tools part of GATK)
4.1.8.1
BaseRecalibrator (GATK)
4.1.8.1
ApplyBQSR (GATK)
4.1.8.1
GroupReadsByUmi (Fgbio)
1.2.0
CollectDuplexSeqMetrics (Fgbio)
1.2.0
CallDuplexConsensusReads (Fgbio)
1.2.0
Fgbio FilterConsensusReads (Fgbio)
1.2.0
0.1.8
Picard CollectAlignmentSummaryMetrics (Picard tools part of GATK)
4.1.8.0