I would like to have the ModeOfInheritence field in the flatfile. about clinvar HOT 7 CLOSED

Interesting... is that field new? I haven't seen it before. At a quick glance it looks like there are >80K values in the file, not sure how many unique variants are actually annotated:

$ gunzip -c ClinVarFullRelease_2016-08.xml.gz | grep ModeOfInheritance | wc -l
   84328

Here are counts of the values in that field:

$ gunzip -c ClinVarFullRelease_2016-08.xml.gz | grep ModeOfInheritance | sed 's/.*\">//' | sed 's/<\/.*//' | sort | uniq -c
51208 Autosomal dominant inheritance
22387 Autosomal recessive inheritance
 951 Autosomal unknown
  49 Codominant
 127 Mitochondrial inheritance
 108 Other
  14 Sex-limited autosomal dominant
1209 Somatic mutation
 317 Sporadic
 947 X-linked dominant inheritance
4542 X-linked inheritance
 997 X-linked recessive inheritance
   5 Xlinked NA
  24 Xlinked recessive
  48 Xlinked unknown
   1 Y-linked inheritance
 158 autosomal dominant
  90 autosomal recessive
1146 autosomal unknown

@bw2 would you by any chance have time to look into this more? If ClinVar is really going to start filling in this field for a large subset of variants then I imagine this is something we'd want to support.

from clinvar.

Yes, our group is also interested in getting these fields annotated with the final TSV results.

THank you!

from clinvar.

Thanks for pointing out ModeOfInheritence. I've added it to the flatfile and vcf as inheritance_modes. The source for it appears to be an optional field in the clinvar submission spreadsheet - currently 19% of variants have it populated.

Also while looking at this, I noticed a couple other fields I hadn't seen before so I added them also:
disease mechanism - this might also be coming from the clinvar submissions spreadsheet (though I couldn't find a field for it).
prevalence and age of onset - clinvar takes these from orphanet.
xrefs - misc. other cross-reference info and ids packed into this column as key:value;key:value;...

I've created a pull request with these changes: #12
Any feedback on the code or data files is appreciated.

from clinvar.

Thank you for the additions. This is definitely helpful. Could you also add the origin info to it? It has germline, de novo and somatic as values for it.

from clinvar.

sure, since the table is changing, I'll add this one also.

from clinvar.

I've added the 'origin' column to PR #12 , and also put in a new 'gold_stars' column which just maps a variant's review_status to a number between 0 - 4. Any feedback is appreciated.

from clinvar.

Thank you again! This is very useful..

from clinvar.