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hardingnj/maskfasta

Last active August 29, 2015 14:00
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Mask regions in fasta where no coverage in a bam file. Useful for calculating null trinucleotide etc distributions
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maskfasta
#!/bin/bash
BAM=this.bam
FASTA=that.fa
OUT=theother.fa
bedtools genomecov -ibam $BAM -bga | awk '$4>0' | bedtools maskfasta -fi $FASTA -bed - -fo $OUT;
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