updated date, fix to filter out SSR variants (suspected false positives)

[jimhavrilla]

Sure. Can do.

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Tue, Aug 22, 2017 at 1:19 PM, Brent Pedersen notifications@github.com wrote:

@brentp commented on this pull request.

can you update the README to indicate what SSR is and why we filter on it. Then at the point in the code where it's used, could you make a short note to the same effect.

Can also be just one line

if v.INFO.get('SSR'): continue

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[jimhavrilla]

Should be up-to-date now.

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Tue, Aug 22, 2017 at 1:20 PM, Jim Havrilla semjaavria@gmail.com wrote:

Sure. Can do.

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Tue, Aug 22, 2017 at 1:19 PM, Brent Pedersen notifications@github.com wrote:

@brentp commented on this pull request.

can you update the README to indicate what SSR is and why we filter on it. Then at the point in the code where it's used, could you make a short note to the same effect.

Can also be just one line

if v.INFO.get('SSR'): continue

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[jimhavrilla]

Done.

Jim Havrilla PhD Candidate in Human Genetics, University of Utah Accelerated BS/MS in Biomedical Engineering, Drexel University '12, Concentration: Bioinformatics "Memory, comprehension, communication, motivation"

On Tue, Aug 22, 2017 at 1:28 PM, Brent Pedersen notifications@github.com wrote:

@brentp commented on this pull request.

In truth-sets/GRCh37/clinvar/make.py https://github.com/quinlan-lab/pathoscore/pull/20#discussion_r134579352:

@@ -32,6 +32,7 @@

exclude things with questionable review status

crs = v.INFO.get('CLNREVSTAT', '').lower() if crs in exclude or any(c in exclude for c in crs.split(",")): continue

• if v.INFO.get('SSR', ''): continue # we filter this out as well, because it indicates a potential false positive variant

can you put the comment above the code? otherwise, this looks good.

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