genome music bmr calc-covg-helper

Question

[qwertyuiop201320142015]

xuhb@xuhb-desktop:~/expirment/exam1$ genome music bmr calc-covg-helper --normal-tumor-bam-pair bam1-list --reference-sequence seq.fa --output-dir ex5   --roi-file roi --normal-min-depth 1 --tumor-min-depth 1 --min-mapq 0 Use of uninitialized value $normal_bam in -s at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm line 143.
Use of uninitialized value $normal_bam in concatenation (.) or string at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm line 143.
Normal BAM file not found or is empty:
Use of uninitialized value $tumor_bam in -s at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm line 144.
Use of uninitialized value $tumor_bam in concatenation (.) or string at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm line 144.
Tumor BAM file not found or is empty:
Use of uninitialized value $normal_bam in -s at /usr/share/perl5/Genome/Model/Tools/Music/Bmr/CalcCovgHelper.pm line 145.
ERROR: Please see 'genome music bmr calc-covg-helper --help' for more information.

When I run calc-covg-helper, it has the above problem.Who can tell me what happened?

Thank u very much

Answer 1

[Cyriac Kandoth]

calc-covg-helper is not meant to be used directly. You need to use calc-covg, which calls calc-covg-helper to help out. It's a code design decision uniquely needed at WashU, where the tool was developed as part of a workflow. calc-covg-helper is a Perl wrapper around the calcRoiCovg binary.

From the error codes, it looks like you have a bug in bam1-list. It needs to be tab-delimited, and use unix- newlines.