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@millerh1

millerh1/shuffle_bam.sh

Created August 27, 2021 22:21
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Shuffle Bam File
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shuffle_bam.sh
#!/bin/bash
bamToBed -i $BAM_ORIG -bed12 -cigar | shuffleBed -i - -g $CHROM_SIZES | bedToBam -bed12 -g $CHROM_SIZES | samtools sort > $BAM_SHUFFLED
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This is a simple one-liner for taking a bam file and shuffling it.

Requires bedtools and samtools installed. Also requires a chrom.sizes file provided for the relevant genome.

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