Convert BAM to BED file format using command line perl

The following command line perl provides an easy way to convert the alignments in a BAM file to BED format.

samtools view file.bam | perl -F'\t' -ane '$strand=($F[1]&16)?"-":"+";$length=1;$tmp=$F[5];$tmp =~ s/(\d+)[MD]/$length+=$1/eg;print "$F[2]\t$F[3]\t".($F[3]+$length)."\t$F[0]\t0\t$strand\n";'

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Last updated on May 06, 2013