Hi,

I'm running the latest version of pindel (0.2.4t) on my BAM of just chromosome 2 reads and I'm getting this error:

$ pindel -i bam_config_file.txt -f /path/to/reference/ -o output_prefix
...
...
Looking at chromosome chr2 bases 10000000 to 20000000.
getReads chr2 263199373
Insertsize in bamreads: 250
Number of reads in current window:                      7490, + 3804 - 3686
Number of reads where the close end could be mapped:    4146, + 2400 - 1738
Percentage of reads which could be mapped: + 63.09% - 47.15%`
BAM file index  0       4146
There are 4146 reads for this chromosome region.
Coordinate of the close end 19994552 is bad.

As a sanity check, the reference I'm passing into pindel is the same same reference used to generate the BAM.

I see that a similar question was posted here, but the response from the pindel author (Kai Ye) was to use the latest version, which I am already: https://trac.nbic.nl/pipermail/pindel-users/2013-April/000247.html

Thank you for any suggestions!