Tools Description

Versions of tools in order of process

Tool	Version
FastqToBam (Fgbio)	1.2.0
SamToFastq (Picard tools part of GATK)	4.1.8.0
Fastp	0.20.1
MergeSamFiles	4.1.8.0
BWA mem	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
ABRA	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
Fgbio Post-processing	0.1.8
Picard CollectAlignmentSummaryMetrics (Picard tools part of GATK)	4.1.8.0