Converting a BAM file to a BED file with bedtools

We can convert a BAM file to a BED file using bedtools.

We have two options:

  • Convert BAM alignments to BED format (using quality as “score”).

    bamToBed -i HG00096.chr20.bam > HG00096.chr20.bed

  • Convert BAM alignments to BED format using edit distance (NM) as the BED “score”.

    bamToBed -i HG00096.chr20.bam -ed > HG00096.chr20.bed[/code]

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