mut column

[dakl]

Hi,

Thanks for this - very useful. I intend to convert this to a VCF file to use downstream. I can't find any info on what the mut columns is. It's value is commonly ALT, but sometimes REF. What does is mean?

thanks!

[dakl]

I've now made a first version of the converter available at dakl/macarthur-clinvar-to-vcf. Feel free to check it out. It currently ignores the mut column form the TSV altogether until I know what to do with it.

thanks

[ericminikel]

mut tells you which allele, the reference or alternate, is the one to which the annotations (e.g. pathogenic assertion) refer.

I guess we should add a data dictionary!

[neilfws]

What about cases where a variant has two or more alternate alleles? These do not seem to be represented in this TSV file.

[ericminikel]

@neilfws they're in there as separate lines, i.e. the dataset is non-unique on chrom, pos, ref:

$ cat output/clinvar.tsv | cut -f1,2,3 | uniq -c | sort -nr | head
  15 3  37067119    T
   8 20 62046495    C
   4 X  153296529   G
   4 3  37089131    A
   4 3  37056036    G
   4 2  47702410    G
   4 2  189860905   G
   4 17 41276033    C
   4 17 41244936    G
   4 17 41219627    G

[hujingchu]

@ericminikel
hi, how can I find the illustration of determining the 'mut' ? It seems Clinvar has not provide such information?
thanks

[ericminikel]

@hujingchu mut was originally (still is?) in the ClinVar XML file, parsed here https://github.com/macarthur-lab/clinvar/blob/master/src/parse_clinvar_xml.py#L62 though I hear the XML format has changed and I haven't kept up so I can't speak to whether it is still in there. ask @bw2 -- he's taken over development of this repo.

[hujingchu]

@ericminikel thank you, I saw the annotations, the method is a little bit strange.
Looking forward @bw2 's advice.

[bw2]

@hujingchu @ericminikel
After spending some time looking into this, I think the mut column is outdated.
The current spreadsheet for submitting variants to clinvar doesn't have instructions for submitting assertions about the REF allele, so I'll remove the mut column from future releases.