#5 bam2cfg.pl generate cfg file with zero size

[Junjiang Lin]

Hi There,

My problem is similar with
https://sourceforge.net/mailarchive/forum.php?thread_name=CACeAgZ0M2ZbwnJYoSPVEtLvXR1_W11V01Df4VYajLo7x9ZQYfw%40mail.gmail.com&forum_name=breakdancer-help

I also used bwa sampe to generate a sam file and then converted it to bam file by samtools.

My command to run bam2cfg.pl is
"perl bam2cfg.pl Swe.bam > Swe.cfg"
but it did not output anything.
Could anyone help me figure this out?

Thanks.
Lin