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create_igv_batch_from_bed.sh
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| #! /bin/bash | |
| #This script takes 2 arguments | |
| #The first script is the BAM file | |
| #The second is the BED file | |
| bam=$1 | |
| bed=$2 | |
| awk -v bam=$bam 'BEGIN { print "new\ngenome hg19\nload "bam"\nsnapshotDirectory ./snapshots/" } { gsub("chr", "", $1); if(NR > 1) print "goto "$1"\t"$2-10"\t"$2+10"\nsort base\ncollapse\nsnapshot"; }' $bed |
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