Problem with gatklite realn when I run seqmule using Iontorrent bam file.

[Majdi NAGARA]

Hi every one,

Please could you help me or suggest me a solution for the WES Iontorrent bam files analysis.

when I run Seqmule using bam file generated from  PGM machine. using this command line:

Seqmule pipeline --bam my-data.bam --platform IonTorrent -e -prefix my-data -threads 8 --capture my-file.bed



I got a problem in the step of gatklite realn.
Have you an idea?

lot of thanks for your help
Majdi