Pindel Segmentation Fault During Sorting and Outputting Tandem Duplications

Question

[Michael]

Hi,

I've been successfully using Pindel on paired end, Illumina MiSeq data aligned with BWA for SV detection. However, running one of my recent samples through the program resulted in a segmentation fault. The last few lines from the terminal says that it occurred during the sorting and outputting tandem duplications step. Here's the output before it terminates:

There are 0 split-reads mapped by aligner.
search far ends
Far end searching completed for this window.
update FarFragName
update FarFragName done
save interchromsome SR
Searching and reporting variations
Reads already used: 0
Far ends already mapped 1329
Checksum of far ends: 220726769
Searching some type of variant, replace this with the correct name in child class ... 
Total: 79    +40    -39
Sorting and outputing deletions ...
Deletions: 474

Searching deletion-insertions ... 
Total: 1715    +823    -892
Sorting and outputing deletions with non-template sequences ...
Added: Sorting and outputing deletions with non-template sequences ...
deletions with non-template sequences: 10

Searching tandem duplication events ... 
Total: 2390    +1282    -1108
Sorting and outputing tandem duplications ...
Segmentation fault

Any help would be appreciated, thanks.

[Danielk]

I've seen that too. I was only able to get rid of the error by turning off tandem dup calling...

[Michael]

You're right, I tried it with the tandem dup parameter set to false and I was able to process the file. I'm using it mainly for it's indel calling so I can ignore this parameter for now.