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Gatk Depthofcoverage Sortbyref.Pl Error

Hi I am trying to run the DepthofCoverage walker from GATK for the first time and I am running into stumbling blocks. I am interested in getting coverage info for genes and I downloaded the Refseq genes list and am filtering and sorting according to specifications. I am using the SortByRef.pl script provided in the website. However, I am getting an error saying: Can not open temporary file 1045: Too many open files at SortByRef.pl line 68, <$INPUT> line 1021.

I am stuck at this point and don't know how to proceed.

Any help is much appreciated.

Thanks

gatk depth-of-coverage exome sequencing
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updated by Biostar Biostar • written by pm2013 • pm2013

1 answer

Your problem is solved here: http://gatkforums.broadinstitute.org/discussion/1328/script-for-sorting-an-input-file-based-on-a-reference-sortbyref-pl

Be sure you restart your computer after modifying the indicated configuration files.

Cheers, Pablo.

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written by pablo.riesgo • pablo.riesgo

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