Tools Used

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