Comments (8)
@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
from clinvar.
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
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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!
from clinvar.
What about cases where a variant has two or more alternate alleles? These do not seem to be represented in this TSV file.
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@ericminikel
hi, how can I find the illustration of determining the 'mut' ? It seems Clinvar has not provide such information?
thanks
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@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.
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@ericminikel thank you, I saw the annotations, the method is a little bit strange.
Looking forward @bw2 's advice.
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@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column is outdated.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.
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Related Issues (20)
- Sometimes "symbol" disagrees with primary hgvs gene annotation HOT 1
- Missing variants HOT 4
- RScript crash HOT 1
- Feature request: Including strand info and genomic start and end coordinates HOT 1
- Wrong gene mapping HOT 2
- Add "last_evaluated" field to VCF
- Improper handling of pseudoautosomal region HOT 1
- Improper labelling of conflicting variants as pathogenic HOT 3
- Job parse failure on system execution. ENV issues? HOT 5
- Another translation for gold stars
- Add LICENSE HOT 2
- Need to Update pathogenic & conflict boolean regex. HOT 1
- ClinSig changes for some halpotypes in join_data.R - become wrong! HOT 2
- Clinical Significance Order Lost in Allele Grouping HOT 8
- Convert the pipeline to hail for .tsv processing steps?
- Augmented tables in output HOT 2
- missing clinvar_alleles_with_exac_v1.*.tsv.gz HOT 1
- Mismatch between clinical_significance_ordered and submitters_ordered HOT 2
- Multiple isoforms not in index
- missing hgvs_c when indel is realigned and shifted.
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