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";'


Last updated on May 06, 2013

ecSeq is a bioinformatics solution provider with solid expertise in the analysis of high-throughput sequencing data. We organize public workshops and conduct on-site trainings on NGS data analysis.

Would you like to receive updates about our NGS trainings and solutions? Then sign-up for our newsletter