5sample.dbm.batch

#!/bin/bash -l
#SBATCH -p shared
#SBATCH -n 1
#SBATCH --mem=60G
#SBATCH -t 120:00:00
#SBATCH --mail-type=END,FAIL         # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=sherwin@txstate.edu    # Where to send mail
#SBATCH --output=slurm-dbm.out

echo "Begin running DBM the time is ----------------------------"

date;

# DBM needs 2 inputs: chr10.snps and chr10.counts

# I only keep the primary alternate allele as multiple alleles is unsupported by Hapseq2
grep -v "#" 5sample.chr10.vcf | awk '{print NR"\t"$1"\t"$2"\t"$6"\t"$4"\t"$5}' > chr10.5sample.snps

# Extract allele count in each sample
grep -v "#" 5sample.chr10.vcf | cut -f 10 | sed 's/:/\t/g' | cut -f 3 | sed 's/,/\t/g' > chr10.10837.count
grep -v "#" 5sample.chr10.vcf | cut -f 11 | sed 's/:/\t/g' | cut -f 3 | sed 's/,/\t/g' > chr10.10855.count
grep -v "#" 5sample.chr10.vcf | cut -f 12 | sed 's/:/\t/g' | cut -f 3 | sed 's/,/\t/g' > chr10.12329.count
grep -v "#" 5sample.chr10.vcf | cut -f 13 | sed 's/:/\t/g' | cut -f 3 | sed 's/,/\t/g' > chr10.12752.count
grep -v "#" 5sample.chr10.vcf | cut -f 14 | sed 's/:/\t/g' | cut -f 3 | sed 's/,/\t/g' > chr10.12878.count

# paste each sample side by side
awk '{print "M\t"NR}' chr10.10837.count | paste - chr10.10837.count chr10.10855.count chr10.12329.count chr10.12752.count chr10.12878.count > chr10.5sample.counts

# DBM haplotypes output to 5sample.g
time /home/s_m774/software/DBM/dbm chr10.5sample > dbmConsoleLog.txt

# Split each sample
sed '1d' chr10.5sample.g > noHeader.chr10.5sample.g
cut -f 4,5 -d ' ' noHeader.chr10.5sample.g > individuals/dbm.genotype.10837.chr10.txt
cut -f 6,7 -d ' ' noHeader.chr10.5sample.g > individuals/dbm.genotype.10855.chr10.txt
cut -f 8,9 -d ' ' noHeader.chr10.5sample.g > individuals/dbm.genotype.12329.chr10.txt
cut -f 10,11 -d ' ' noHeader.chr10.5sample.g > individuals/dbm.genotype.12752.chr10.txt
cut -f 12,13 -d ' ' noHeader.chr10.5sample.g > individuals/dbm.genotype.12878.chr10.txt

echo "After running DBM, the time is ----------------------------"

date;