bam2pindel Error

[Medhat]

Hi,

I am trying to use bam2pindel using this command:
perl bam2pindel.pl -i ./sorted_ByName.bam -o ./pindel -s s79757 -pi 400

It gives me this error:

Forked pipe to run: /home/medhat/bin/samtools view sorted_ByName.bam
Error while processing: /home/medhat/bin/samtools view sorted_ByName.bam
EVAL ERROR: Use of uninitialized value in array element at /home/medhat/source/pindel/pindel/Adaptor.pm line 92, <$PROC> line 1.

CHILD ERROR: 0

Reads in buffer:
$VAR1 = [];

Broke at record 1
 at bam2pindel.pl line 341
	main::run_parser('HASH(0x18ac4e0)') called at bam2pindel.pl line 83

any idea?
Thanks in advance

[BurgundiaPR]

Hi,

I have exactly the same problem. Did you manage to fix it ? If yes, how ?
If other people have an idea on what can explain it, their help is welcomed

Thanks to all

[emucaki]

Bumping this, as I am getting the exact same message and I haven't been able to find any mention of this error elsewhere on the internet.

My data is aligned using BWA, converted to a BAM file using samtools normally, and sorted the way the program suggests.

Any help would be welcomed.

[Lillianwu0314]

Hi all,

Very late to the party. I've been getting the same error message when trying to run bam2pindel. Has anyone managed to solve it? I emailed Kai Ye but he has yet to reply.