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stevekm / reportIT

IonTorrent variant reporting pipeline for clinical interpretation of cancer panel results
GNU General Public License v3.0
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WC PMKB Excel sheet variant parsing needed #7

Closed stevekm closed 7 years ago

stevekm commented 7 years ago

In order to integrate clinical interpretations of variants from the WC PMKB database (here: https://pmkb.weill.cornell.edu/therapies/download.xlsx , https://pmkb.weill.cornell.edu/), the provided Excel sheet needs to be parsed to make searching for variants easier. Current scripts only provide TSV output format, but scripts need to be extended to split the dataset so each individiual variant has a single row, and the variant ID's match ANNOVAR output format.

stevekm commented 7 years ago

Further parsing down the Excel table may not be helpful since the tumor and tissue type information is still not available for matching with interpretations. Once this information is available, it may be possible to still successfully parse the table for matching entries without further parsing needed.