File: primer_bam_to_bed.sh

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#!/bin/bash

c=$1
p=$2
r=$3

cut -f 1,2 -d ',' $c | sed 's/^/>/g' | tr ',' '\n' > ${p}.fa
~/Documents/bwa/bwa mem -k 5 -T 20 $r ${p}.fa | samtools view -bS -F 4 -o ${p}.bam # Tune -T parameter.
bedtools bamtobed -i ${p}.bam > ${p}.bed