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Tools Description

Versions of tools in order of process

Tool

Version

(Fgbio)

1.2.0

(Picard tools part of GATK)

4.1.8.0

0.20.1

4.1.8.0

0.7.17

(Picard tools part of GATK)

4.1.8.1

(Picard tools part of GATK)

4.1.8.0

(Picard tools part of GATK)

4.1.8.1

(Bedtools)

2.28.0_cv2

(Bedtools)

2.28.0_cv2

2.22

(Picard tools part of GATK)

4.1.8.1

(GATK)

4.1.8.1

(GATK)

4.1.8.1

(Fgbio)

1.2.0

(Fgbio)

1.2.0

(Fgbio)

1.2.0

(Fgbio)

1.2.0

0.1.8

(Picard tools part of GATK)

4.1.8.0

MergeSamFiles

AddOrReplaceReadGroups

MergeBamAlignment

MarkDuplicates

ABRA

FixMateInformation

BaseRecalibrator

GroupReadsByUmi

CollectDuplexSeqMetrics

CallDuplexConsensusReads

Fgbio FilterConsensusReads

Fgbio Post-processing

Picard CollectAlignmentSummaryMetrics