scalpel on bam generated with gatk best practices .

[anand_mt]

Hello,

I am using scalpel 0.2.1(beta), and I have some questions.

1. Will scalpel work on bam file processed with GATK best practices approach?

   remove dups > local realignment around indels > BQSR

2. I am getting this error in --somatic mode:

command: scalpel --somatic --normal Normal_recal.bam --tumor Tumor_fsorted.bam --bed Exome_Covered.bed --ref hg19.fa --mapscore 25 --dir ./scalpel_indel/ --numprocs 6 --format annovar --intarget --mincov 10

Loading targets from BED file...185636 targets (filtered 0 overlapping).
Loading genome from FASTA file...25 sequences.
Assembly Exons
start assembly of 401216 regions.
stepSize: 66870
1. [0..66869]
2. [66870..133739]
3. [133740..200609]
sh: 1: Syntax error: Bad fd number
Command failure: microassembly (... )...
child exited with value 2

First I thought may be something to do with bam file, since it was processed with GATK, but its the same error with raw bam.

Thank you.

[SaiZheng]

I have this problem in my calling,have you solve it?please