bqsr_recal_make_input.sh

#!/bin/bash

##########################################################################
#
# Platform: NCI Gadi HPC
# Usage: bash bqsr_recal_make_input.sh <config prefix>
# Version: 2.0
#
# For more details see: https://github.com/Sydney-Informatics-Hub/Fastq-to-BAM
#
# If you use this script towards a publication, please acknowledge the
# Sydney Informatics Hub (or co-authorship, where appropriate).
#
# Suggested acknowledgement:
# The authors acknowledge the support provided by the Sydney Informatics Hub,
# a Core Research Facility of the University of Sydney. This research/project
# was undertaken with the assistance of resources and services from the National
# Computational Infrastructure (NCI), which is supported by the Australian
# Government, and the Australian BioCommons which is enabled by NCRIS via
# Bioplatforms Australia funding.
#
##########################################################################

cohort=../$1

group=true

if [[ $group =~ true ]]; then
	printf "Creating group-based BQSR recalibration inputs from ${cohort}.config\n"
else
	printf "Creating BQSR recalibration inputs from ${cohort}.config, no sample grouping applied\n"
fi

t_input=./Inputs/bqsr_recal.inputs-tumour
n_input=./Inputs/bqsr_recal.inputs-normal
input=./Inputs/bqsr_recal.inputs

rm -f $t_input
rm -f $n_input
rm -f $input

intervals=$(ls -1 ../Reference/BQSR_intervals/*list) #directory of text files generated by GATK SplitIntervals
intervals=($intervals)

# Collect sample IDs from cohort.config
while read -r sampleid labid seq_center library; do
        if [[ ! ${sampleid} =~ ^#.*$ ]] 
	then
                if [[ $group =~ true ]]; then
                       if [[ $labid =~ -N|-B ]]; then
                                samples_n+=("${labid}")
                        else
                                samples_t+=("${labid}")
                        fi
                else
                        samples+=("${labid}")
                fi
        fi
done < "${cohort}.config"

for n_sample in ${samples_n[@]}; do
        for ((i=0;i<${#intervals[@]};i++))
        do
                printf "${n_sample},${i},${intervals[i]}\n" >> ${n_input}
        done
done

for t_sample in ${samples_t[@]}; do
        for ((i=0;i<${#intervals[@]};i++))
        do
                printf "${t_sample},${i},${intervals[i]}\n" >> ${t_input}
        done
done

for sample in ${samples[@]}; do
        for ((i=0;i<${#intervals[@]};i++))
        do
                printf "${sample},${i},${intervals[i]}\n" >> ${input}
        done

done


if [ -f $input ]
then
        tasks=`wc -l < $input`
        printf "Number of BaseRecalibrator tasks to run: ${tasks}\n"
fi

if [ -f $n_input ]
then
        tasks=`wc -l < $n_input`
        printf "Number of BaseRecalibrator normal sample tasks to run: ${tasks}\n"
fi

if [ -f $t_input ]
then
        tasks=`wc -l < $t_input`
        printf "Number of BaseRecalibrator tumour sample tasks to run: ${tasks}\n"
fi

printf "\n!!! Before running bqsr_recal_run_parallel.pbs, edit the script and unhash the correct task script for human/non-human samples\n"
printf "If you're using the non-human script, remember to fill in the \$dbsnp variable\n"