Shruti Paniwala
A Bioinformatician
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QV calculation in Bash !
By Shruti Paniwala 1601 days ago
# $1 = vcf file
# $2 = input bam file
# $3 = output QV file
module load samtools
NUM_BP=`samtools depth $2 | perl -e '$c = 0; while(<>){chomp; @s = split(/\t/); if(scalar(@s) >= 3){$c++;}} print "$c\n";'`
echo "num bp: "$NUM_BP
NUM_SNP=`cat $1 |grep -v "#" | awk -F "\t" '{if (!match($NF, "0/1")) print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$8}' | tr ';' ' ' | sed s/AB=//g | awk -v WEIGHT=0 '{if ($6 >= WEIGHT) print $0}' | awk -v SUM=0 '{if (length($4) == length($5)) { SUM+=length($4); } else if (length($4) < length($5)) { SUM+=length($5)-length($4); } else { SUM+=length($4)-length($5)}} END { print SUM}'`
echo "num snp: "$NUM_SNP
perl -e 'chomp(@ARGV); $ns = $ARGV[0]; $nb = $ARGV[1]; print (-10 * log($ns/$nb)/log(10)); print "\n";' $NUM_SNP $NUM_BP > $3
cat $3
