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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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Missing Polyphen in hg19/hg38? #63

Closed scchess closed 5 years ago

scchess commented 5 years ago

The Polyphen scoring seem to be missing in both hg19/hg38. For example:

wget http://www.openbioinformatics.org/annovar/download/hg19_dbnsfp35c.txt.gz
gunzip hg19_dbnsfp35c.txt.gz
grep Polyphen hg19_dbnsfp35c.txt | wc

0 line counted.

On http://annovar.openbioinformatics.org/en/latest/misc/accessory, it says there should be a "Polyphen" column, but there shouldn't.

Should we add Polyphen back?

kaichop commented 5 years ago

You can check the first row of the file which should list all columns. polyphen should be there but the name may not be "Polyphen" exactly.

On Sun, May 12, 2019 at 11:33 PM student-t notifications@github.com wrote:

The Polyphen scoring seem to be missing in both hg19/hg38. For example:

wget http://www.openbioinformatics.org/annovar/download/hg19_dbnsfp35c.txt.gz gunzip hg19_dbnsfp35c.txt.gz grep Polyphen hg19_dbnsfp35c.txt | wc

On http://annovar.openbioinformatics.org/en/latest/misc/accessory, it says there should be a "Polyphen" column, but there shouldn't.

Should we add Polyphen back?

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