run pindel with re-aligned bam files?

[caswater]

Hi, when I am using pindel to call indels from the bam files, I am just wondering if I shall feed the program with the duplicate-removed bam files, or should I use the re-aligned and re-calibrated bam files after GATK processing?

Thanks for your advice

[Heisman]

It shouldn't matter, although if anything I would use the re-aligned files. Pindel considers mainly your paired end reads that have only one end align; that shouldn't be affected much by the indel realignment, I don't think.

[caswater]

Thanks a lot. So I'll go with the realigned bam then. Thanks!