pindel somatic indel filter

Question

[Leandro de Mattos]

I'm trying to use the script (https://github.com/genome/pindel/tree/master/somatic_filter/somatic_indelfilter.pl) perl /root/pindel/somatic_filter/somatic_indelfilter.pl somatic.indel.filter.config

My result is informing that it has no reads, but is not trure, because the reads are there. The output (example):

• Chromosomes in which SVs have been found: Scanning chromosome: chr1 Scanning chromosome: chr2 Scanning chromosome: chr3 Scanning chromosome: chr4 Scanning chromosome: chr5 Scanning chromosome: chr6 Scanning chromosome: chr7 Scanning chromosome: ...... No reads for chromosome chr1, skipping it. Removing chromosome chr1 from memory. No reads for chromosome chr2, skipping it. Removing chromosome chr2 from memory. No reads for chromosome chr3, skipping it. Removing chromosome chr3 from memory. No reads for chromosome chr4, skipping it. Removing chromosome chr4 from memory. No reads for chromosome chr5, skipping it.

Does anyone have any suggestions? Or any way to filter pindel output?