Pindel Error: Shiftedvector Out-Of-Range Error

Question

[snap.city.major]

Hello,

I’ve been running pindel like so: pindel --config-file bam_config.txt --fasta /path/to/hg19/fasta/ --chromosome ALL --output-prefix /path/to/output

and I’ve noticed a lot of my pindel jobs fail with this error message: ShiftedVector out-of-range error: position 10096801 falls outside range 10099480-15100520

I’m using Pindel version 0.2.5, June 4 2013.

I was unable to find other posts relating to this error so any suggestions/help would be much appreciated. Thank you.

Answer 1

[liangkaiye]

removed the code causing the problem. can you check out the latest version at github.com/genome/pindel?

[snap.city.major]

Thank you, Kai. Updating to version 0.2.5a1 fixes this problem.

On an unrelated note, I noticed that the '--include' option allows users to specify a BED file and pindel will consider indels only in those regions. However, I noticed that pindel seems to be only reading the first line in the BED file and ignoring the rest.

For example, if I have three coordinate regions in my BED and only one of those regions contain an indel, the indel is only called when that region is FIRST in the BED file. Could you comment?

[snap.city.major]

FIXED: the BED file specified by --include should only have the required BED columns: chrom, bed start, bed end.

Answer 2

[angadps]

Hello Kai,

I'm sort of trying to do the same thing as snap.city is where I have a bed file, and intend to call indels only in certain regions. However, I run into multiple problems:

Can you tell us what the expected format is for the bed file? I've tried the following:

Tab-separated regions such as:

chr1 345345 346345 or 1 345345 346345

Non-tab-separated such as:

chr1:345345-346345 or 1:345345-346345

I end up getting either a Segmentation fault, or no calls at all. I get segfaults with using tab-separated list, and no calls when using the other. The latter could also mean only the first line in the bed file is picked up. However, I placed a region with a definitive indel at top and tried running with --include but it failed to report the indel (It does report with -c though). I've tried both the 'chr1' and '1' naming types since when I directly specify the region using -c, chr as '1' works well. However, nothing seems to work. I'm trying the latest pindel version : Pindel version 0.2.5a3, Oct 24 2013. Your help is appreciated here.

Thanks.