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tgen / CovGen

Creates a target specific exome_full192.coverage.txt file required by MutSig
MIT License
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KeyError: 'chrY' #6

Closed phuchoang1012 closed 6 years ago

phuchoang1012 commented 6 years ago

Hello,

I am running CovGen to generate compatible coverage file for hg38: /tools/CovGen-master/CovGen -o out -f GRCh38.fa -g Homo_sapiens.GRCh38.93.chr.gtf -t -t Exome-Agilent_V6_UTR_b38_merge.bed -s /apps/snpeff/4.3t/snpEff/ -v GRCh38.86

I encountered the following error: Traceback (most recent call last): File "/tools/CovGen-master/getALTsForTargetsSeqsForMutSig.py", line 352, in lseqs, lseqs_coord = parseBedFile(bedf, dict_fasta, naturalSortBedLoci) File "/tools/CovGen-master/getALTsForTargetsSeqsForMutSig.py", line 178, in parseBedFile logger.debug(id + " : " + str(len(dict_fasta[id]))) KeyError: 'chrY'

I wonder if you could offer some insights on this error and how to fix it. Thank you very much in advance for your help!

awchrist commented 6 years ago

Are you using a UCSC reference genome? UCSC uses "chr" in front of the chromosome. If you remove the "chr" from the reference fasta it should work.