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griffithlab / pVACtools

http://www.pvactools.org
BSD 3-Clause Clear License
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Minor fix in readme #1066

Closed serge2016 closed 6 months ago

serge2016 commented 6 months ago

Hello!

If I understand correctly, here it is about specifically somatic VCFs from strelka2, but not about germline: https://github.com/griffithlab/pVACtools/blob/9642052ba082641ed2d2fd43bbcbdbe12110d4ed/docs/pvacseq/input_file_prep/gt.rst?plain=1#L12 I suppose to add word somatic in this sentence.

serge2016 commented 6 months ago

I am not sure that --fasta is necessary, if it is already installed: https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#fasta

https://github.com/griffithlab/pVACtools/blob/9642052ba082641ed2d2fd43bbcbdbe12110d4ed/docs/pvacseq/input_file_prep/vep.rst?plain=1#L47

I suppose it should also be mentioned

susannasiebert commented 6 months ago

I am not sure that --fasta is necessary, if it is already installed: https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#fasta

I believe it is required when specifying the --hgvs option, regardless of whether or not a a cache directory is specified.

From your link:

The cache does not store any information pertaining to, and therefore cannot be used for, the following:

  • HGVS names (--hgvs, --hgvsg) - to retrieve these you must additionally point to a FASTA file containing the reference sequence for your species (--fasta)
susannasiebert commented 6 months ago

Hello!

If I understand correctly, here it is about specifically somatic VCFs from strelka2, but not about germline:

https://github.com/griffithlab/pVACtools/blob/9642052ba082641ed2d2fd43bbcbdbe12110d4ed/docs/pvacseq/input_file_prep/gt.rst?plain=1#L12

I suppose to add word somatic in this sentence.

This has been updated. Closing this issue.