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Illumina / GTCtoVCF

Script to convert GTC/BPM files to VCF
Apache License 2.0
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Script reports that reference has missing chromosome 6 #8

Closed YourLogoHere closed 6 years ago

YourLogoHere commented 6 years ago

Is there a known cause for why the script will report the following error upon execution?

"2018-03-01 16:51:29,607 - GTC converter - ERROR - FASTA reference is missing entry for chromosome 6"

This seems to only be a problem with the GrCh38 reference; it seems to work fine with build 37.

YourLogoHere commented 6 years ago

I forgot to add that this error seems to be inconsistent with regard to which chromosome it says it's missing --- running it multiple times has given reports of the reference missing chr 3, 12, etc.

KelleyRyanM commented 6 years ago

In your reference file, is chromosome 6 named as "6" or "chr6"?

YourLogoHere commented 6 years ago

Ah; that was it --- was using hg38 rather than GrCh38. Just as a heads up though, the FTP link provided in the README has the contigs with the "chr" prefix, even though it's ostensibly GrCh38 --- that was what ended up confusing me; I didn't check the reference beforehand.

KelleyRyanM commented 6 years ago

Thank you for noting this issue. The documentation has been updated to reference a newly added script that can be used to build the appropriate reference sequence.