Error: Running pindel on breakdancer output

[opulcy97]

Hi All,

I am running breakdancer output in pindel and getting errors. My command is as follows:

pindel -f human_g1k_v37.fasta -i Sample.config.txt -o Sample.chr11 -c 11 -b Sample.ctx

I am getting the following errors which produces empty pindel SV files:
.............................................................................
Looking at chromosome 11 bases 0 to 5000000.
[bam_index_load] wrong magic number.
*** glibc detected *** pindel: double free or corruption (!prev): 0x000000001ef65800 ***
..............................................................................
This is followed by something like "Backtrace" and "Memory map"

I am using 0.2.4x of May 8, 2013

Can anyone please tell me what seems to be the problem? I looked around and it looks like no one has ever faced the problem. I have also tried different setting but couldn't manage to solve the problem.

Your help is always appreciated.

Many thanks in advance.

Regards

[KaiYe]

can you try the newest Pindel version at
github.com/genome/pindel

[opulcy97]

Hi Kai,

I will try to run that and let you know what's going on. In past I had difficulties installing Pindel in my local machine. However, my admin installed it for me. I will give another try by myself and if not will request the admin. I will keep you posted.

Regards