Dindel Realining Reads

[bnfoguy]

Hello,

I am using to call indels from cancer data. So far I have been successfull with Stage 1, 2 & 3. When I try to use the mergeOutpuDiploid in stage 4, I get the following error:


./mergeOutputDiploid.py --inputFiles /home/ryajnik/binaries/ERR035488_cutfile.dindel_stage2_output_windows.2.glf.txt --outputFile v
ariantCalls.VCF --ref /home/ryajnik/samtools-0.1.18/genome.fa
WARNING: additional columns in line 1 of file /home/ryajnik/binaries/ERR035488_cutfile.dindel_stage2_output_windows.2.glf.txt were ignored
File msg does not exist
. Aborting.
An error occurred!


Can anyone point me on how to troubleshoot?

Thanks,

[Heisman]

Dindel is hard to troubleshoot, but I've made it work. Could you maybe post a few lines of the files it is trying to merge and I'll compare those to ones I have when it runs smoothly?

Also, when you get a few lines together, put those specific lines into new files in a separate directory and then run it on just those few lines to make sure you get the same error. If there's say only one line among all your files that is causing the problem and you don't show me that line, then we won't get anywhere.

[bnfoguy]

This is the output I get after running the mergeoutputdiploid command:

[ryajnik@bayes dindel-1.01-python]$ ./mergeOutputDiploid.py --inputFiles /home/ryajnik/binaries/ERR035488_cutfile_sorted.dindel_stage2_outputfiles.txt --outputFile variantCalls.VCF --ref /home/ryajnik/samtools-0.1.18/genome.fa
WARNING: additional columns in line 1 of file /home/ryajnik/binaries/ERR035488_cutfile_sorted.dindel_stage2_outputfiles.txt were ignored
File msg does not exist
. Aborting.

I cannot go any further than that.

Thanks,