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zwdzwd / transvar

TransVar - multiway annotator for precision medicine
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ganno batch example #12

Closed cboustred closed 7 years ago

cboustred commented 7 years ago

Please could you post an example of a ganno (genomic co-ordinates to HGVS) batch input example file and the command I would use to run it?

e.g. if I had a file a bit like this (only a quick example)

# chrom pos ref alt preferred_transcript
chr6 1234 A T ENST001234
chr10 4321 A C ENST004321
etc...

Whats the ganno command to run to run transvar and return the corresponding HGVS co-ordinates?

Thanks in advance!

zwdzwd commented 7 years ago

Hi, I updated the document with two examples, http://transvar.readthedocs.io/en/latest/annotation_from_genomic_level.html#batch-processing Also I found a problem while parsing using "-a". So I updated the code as well. if you find an issue, try update your install.

Thanks