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quinlan-lab / pathoscore

pathoscore evaluates variant pathogenicity tools and scores.
MIT License
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added aloft score #28

Closed jimhavrilla closed 7 years ago

brentp commented 7 years ago

actually, I guess it should be usable by vcfanno with multiple alts per line...

jimhavrilla commented 7 years ago

So to clarify you want those 7 columns and to rm the gz files

On Sat, Sep 2, 2017 at 11:29 AM Brent Pedersen notifications@github.com wrote:

actually, I guess it should be usable by vcfanno with multiple alts per line...

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/quinlan-lab/pathoscore/pull/28#issuecomment-326758449, or mute the thread https://github.com/notifications/unsubscribe-auth/AGQ8BBshaZgte0e1h9XshWl7kZ2Z6Gi1ks5seZB5gaJpZM4PKsQt .

-- 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"

brentp commented 7 years ago

yes. and you can leave all 3 alts on one line. would you just test that you can annotaed e.g some clinvar pathogenics with this score via vcfanno and it does the expected ref/alt matching?

jimhavrilla commented 7 years ago

I can just split it if you want

On Sat, Sep 2, 2017 at 12:14 PM Brent Pedersen notifications@github.com wrote:

yes. and you can leave all 3 alts on one line. would you just test that you can annotaed e.g some clinvar pathogenics with this score via vcfanno and it does the expected ref/alt matching?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/quinlan-lab/pathoscore/pull/28#issuecomment-326761098, or mute the thread https://github.com/notifications/unsubscribe-auth/AGQ8BIDeFN76bHmmNOx1Qt-UewyDSMZVks5seZrogaJpZM4PKsQt .

-- 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"

brentp commented 7 years ago

I think it's better not to split if it's not needed.

jimhavrilla commented 7 years ago

I’ll test it then

On Sat, Sep 2, 2017 at 12:35 PM Brent Pedersen notifications@github.com wrote:

I think it's better not to split if it's not needed.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/quinlan-lab/pathoscore/pull/28#issuecomment-326762213, or mute the thread https://github.com/notifications/unsubscribe-auth/AGQ8BF18QMSaDrt_5vIzIUB18axXTWinks5seZ_XgaJpZM4PKsQt .

-- 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"

jimhavrilla commented 7 years ago

It works.

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 Sat, Sep 2, 2017 at 12:35 PM, Jim Havrilla semjaavria@gmail.com wrote:

I’ll test it then

On Sat, Sep 2, 2017 at 12:35 PM Brent Pedersen notifications@github.com wrote:

I think it's better not to split if it's not needed.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/quinlan-lab/pathoscore/pull/28#issuecomment-326762213, or mute the thread https://github.com/notifications/unsubscribe-auth/AGQ8BF18QMSaDrt_5vIzIUB18axXTWinks5seZ_XgaJpZM4PKsQt .

-- 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"

jimhavrilla commented 7 years ago

I'll change the format then.

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 Sat, Sep 2, 2017 at 12:57 PM, Jim Havrilla semjaavria@gmail.com wrote:

It works.

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 Sat, Sep 2, 2017 at 12:35 PM, Jim Havrilla semjaavria@gmail.com wrote:

I’ll test it then

On Sat, Sep 2, 2017 at 12:35 PM Brent Pedersen notifications@github.com wrote:

I think it's better not to split if it's not needed.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/quinlan-lab/pathoscore/pull/28#issuecomment-326762213, or mute the thread https://github.com/notifications/unsubscribe-auth/AGQ8BF18QMSaDrt_5vIzIUB18axXTWinks5seZ_XgaJpZM4PKsQt .

-- 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"

jimhavrilla commented 7 years ago

done