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]