Parallel SNP calling by chromosome

parallelMpileup.sh

#!/bin/bash
NUM_THREADS=$(getconf _NPROCESSORS_ONLN)
REF="MyReference.fa"
BAMFILE_SORTED="MySortedAndIndexed.bam"
VCF_FILE="My.vcf"

# Parallel SNP calling by chromosome
bcftools mpileup -r chr1 -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0 > chr1_${VCF_FILE}.gz &
bcftools mpileup -r chr2 -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0 > chr2_${VCF_FILE}.gz &
bcftools mpileup -r chr3 -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0 > chr3_${VCF_FILE}.gz &
bcftools mpileup -r chr4 -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0 > chr4_${VCF_FILE}.gz &
bcftools mpileup -r chr5 -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0 > chr5_${VCF_FILE}.gz &
bcftools mpileup -r chr6 -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0 > chr6_${VCF_FILE}.gz &
bcftools mpileup -r chr7 -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0 > chr7_${VCF_FILE}.gz &
bcftools mpileup -r chr8 -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0 > chr8_${VCF_FILE}.gz &
bcftools mpileup -r chr9 -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0 > chr9_${VCF_FILE}.gz &
bcftools mpileup -r chr10 -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0 > chr10_${VCF_FILE}.gz &
bcftools mpileup -r chr11 -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0 > chr11_${VCF_FILE}.gz &
bcftools mpileup -r chr12 -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0 > chr12_${VCF_FILE}.gz &
bcftools mpileup -r chr13 -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0 > chr13_${VCF_FILE}.gz &
bcftools mpileup -r chr14 -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0 > chr14_${VCF_FILE}.gz &
bcftools mpileup -r chr15 -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0 > chr15_${VCF_FILE}.gz &
bcftools mpileup -r chr16 -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0 > chr16_${VCF_FILE}.gz &
bcftools mpileup -r chr17 -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0 > chr17_${VCF_FILE}.gz &
bcftools mpileup -r chr18 -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0 > chr18_${VCF_FILE}.gz &
bcftools mpileup -r chr19 -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0 > chr19_${VCF_FILE}.gz &
bcftools mpileup -r chr20 -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0 > chr20_${VCF_FILE}.gz &
bcftools mpileup -r chr21 -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0 > chr21_${VCF_FILE}.gz &
bcftools mpileup -r chr22 -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0 > chr22_${VCF_FILE}.gz &
bcftools mpileup -r chrX -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0  > chrX_${VCF_FILE}.gz &
bcftools mpileup -r chrY -Ou -C 50 -f $REF $BAMFILE_SORTED | bcftools call -O z --threads $NUM_THREADS -v -V indels -m -P 0  > chrY_${VCF_FILE}.gz &
wait

# Concatenate all chromosome VCFs to one big file
bcftools concat -O z chr[1-9]_${VCF_FILE}.gz chr[1-2][0-9]_${VCF_FILE}.gz chr[M,X-Y]_${VCF_FILE}.gz > ${VCF_FILE}.gz
tabix ${VCF_FILE}.gz

# Delete no longer needed VCFs
rm -f chr[1-9]_${VCF_FILE}.gz chr[1-2][0-9]_${VCF_FILE}.gz chrX_${VCF_FILE}.gz