how to bypass Pindel error
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5.5 years ago
genya35 ▴ 40

Hello,

Could someone pleases suggest hot to interpret and bypass the following Pindel error:

I'm running Pindel on a 25 small indexed bam files for PDGFRA e12 (Ion Torrent) using chr4 reference.

1. I build a list of all the files and insert size
2. I run pindel: $pindel -f$fastafile -i $configfile -c ALL -o$outputfolder";
3. I run pindeltovcf: $pindeltovcf -p$deloutput -r $fastafile -R hg19-GRCh37 -d 200903 -v$delvcf"

For the most part it is working very well. The problem is that Pindel crashes when it encounters a bad bam file. Is there a setting that will allow Pindel to continue analyzing other good file and not to crash?

Thank you.

software error • 1.1k views
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Although this is not an answer, you should try validating your bam/sam files with picard tools ( http://broadinstitute.github.io/picard/command-line-overview.html#ValidateSamFile) before your run pindel on it. Unless it is a bug in pindel, a bad bam is not good for downstream analysis. They are supposed to be fixed, IMHO.

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by bad I mean if a particular sample failed and bam has no reads.