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macarthur-lab / clinvar

This repo provides tools to convert ClinVar data into a tab-delimited flat file, and also provides that resulting tab-delimited flat file.
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Request: Adding Benign column to the output #15

Closed vigneshravi closed 8 years ago

vigneshravi commented 8 years ago

Hi,

Can a benign column and a conflicts column (just like Pathogenic and Conflicting_Pathogenicity) be added to the results?

bw2 commented 8 years ago

Adding a benign column sounds good to me. It'll = 1 if the variant has been asserted benign or likely benign by at least one clinvar submitter.

As far as another 'conflicted' column, correct me if I'm wrong, but the existing 'conflicted' column should already work as is. It = 1 when there are 'benign / likely benign' and 'pathogenic / like pathogenic' assertions for a variant.

vigneshravi commented 8 years ago

That's ture! Just a benign column sounds good.. Thank you!

bw2 commented 8 years ago

Actually, conflicted will = 1 if/only if both pathogenic = 1 and benign= 1 so the conflicted column becomes completely redundant. I don't mind keeping it for convenience though.

vigneshravi commented 8 years ago

Pathogenic=1 if ClinVar_clinical_significance==Pathogenic or Likely Pathogenic or Risk Factor Benign=1 if ClinVar_clinical_significance==Benign or Likely Benign or Protective Conflicted=1 if P/LP and B/LB are seen together

Can you also add a column if there is "no conflicts" in ClinVar_review_status? This will clear up variants where P/LP is reported by one submitter and uncertain significant is submitted by another submitter. This column will be a filter on top of the previous three to really pull out unconflicted pathogenic variants.

Just a thought! Thanks for being super responsive to requests. Really appreciate this!

On Wed, Sep 21, 2016 at 4:44 PM, bw2 notifications@github.com wrote:

Actually, conflicted will = 1 if/only if both pathogenic = 1 and benign= 1 so the conflicted column becomes completely redundant. I don't mind keeping for convenience though.

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bw2 commented 8 years ago

I think these additional 1/0 columns besides benign are too niche and users that need them can just calculate them from the other fields. Also, 'Risk Factor' and 'Protective' are not currently considered when computing the pathogenic and conflicted columns. I'm not sure if there's a good reason to change this.

vigneshravi commented 8 years ago

I see.. I guess the benign for now is good.

On Wed, Sep 21, 2016 at 6:13 PM, bw2 notifications@github.com wrote:

I think these additional 1/0 columns besides benign are too niche and users that need them can just calculate them from the other fields. Also, 'Risk Factor' and 'Protective' are not currently considered when computing the pathogenic and conflicted columns. I'm not sure if there's a good reason to change this.

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vigneshravi commented 8 years ago

Thank You!