Using BWA:
*mapping_scripts/*
map-HG00096-orig-1.sh: Mapping HG00096 (original order)
map-HG00096-shuf-1.sh: Reshuffling and mapping HG00096 (shuffled order)
map-HG02107-orig.sh: Mapping HG02107 (original order)
map-HG02107-shuf.sh: Reshuffling and mapping HG02107 (shuffled order)
map-exome-1.sh: Mapping exomes in original order
*variant_caller_scripts/*
GATK-call-HG00096-orig-1.sh: SNV+Indels using GATK. HG00096, original order.
GATK-call-HG00096-orig-2.sh: SNV+Indels using GATK. HG00096, original order - rerun.
GATK-call-HG00096-shuf-1.sh: SNV+Indels using GATK. HG00096, shuffled order.
GATK-call-HG02107-1.sh: SNV+Indels using GATK. HG02107, original order.
GATK-call-HG02107-2.sh: SNV+Indels using GATK. HG02107, original order - rerun.
GATK-call-HG02107-shuf.sh: SNV+Indels using GATK. HG02107, shuffled order.
GATK-call-exome-1.sh: SNV+Indels using GATK. WES datasets, original order.
GATK-call-exome-2.sh: SNV+Indels using GATK. WES datasets, original order - rerun.
Freebayes-call.sh: SNV+Indels using Freebayes.
Platypus-call.sh: SNV+Indels using Platypus.
SAMTools-call.sh: SNV+Indels using SAMtools.
DELLY-call.sh: SV using DELLY.
LUMPY-call.sh: SV using LUMPY.
genomestrip-HG00096.sh: SV using Genome STRiP (HG00096).
genomestrip-HG02107.sh: SV using Genome STRiP (HG02107).
vcfAnalysisRuns.sh: Comparison of VCF files.
Makefile: to run them all
*read_shuffler/*
Makefile
shuffle-fastq.c