Versions of tools in order of process
Tool
Version
FastqToBamarrow-up-right (Fgbio)
1.2.0
SamToFastqarrow-up-right (Picard tools part of GATK)
4.1.8.0
Fastparrow-up-right
0.20.1
MergeSamFilesarrow-up-right
BWA memarrow-up-right
0.7.17
AddOrReplaceReadGroupsarrow-up-right (Picard tools part of GATK)
4.1.8.1
MergeBamAlignmentarrow-up-right (Picard tools part of GATK)
MarkDuplicatesarrow-up-right (Picard tools part of GATK)
GenomeCovarrow-up-right (Bedtools)
2.28.0_cv2
Mergearrow-up-right (Bedtools)
ABRAarrow-up-right
2.22
FixMateInformationarrow-up-right (Picard tools part of GATK)
BaseRecalibratorarrow-up-right (GATK)
ApplyBQSRarrow-up-right (GATK)
GroupReadsByUmiarrow-up-right (Fgbio)
CollectDuplexSeqMetricsarrow-up-right (Fgbio)
CallDuplexConsensusReadsarrow-up-right (Fgbio)
Fgbio FilterConsensusReadsarrow-up-right (Fgbio)
Fgbio Post-processingarrow-up-right
0.1.8
Picard CollectAlignmentSummaryMetricsarrow-up-right (Picard tools part of GATK)
Last updated 5 years ago
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