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zjshi / gt-pro

MIT License
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no chrom in output? #2

Closed snayfach closed 5 years ago

snayfach commented 5 years ago

head snp_dict.tsv

species_id pos ref alt

206814 23513 G A 206814 23774 G A 206814 25401 T G 206814 25618 G C

I was expecting a chrom column indicating the contig on which a SNP is found. Otherwise I don't know where each SNP is found relative to the representative genome. This is useful for me personally so I can match (a) the true genotype of a new genome versus (b) the predicted genotype based on the output of gtpro

Maybe this information is contained in the parsed output. I will try running the tool to see

zjshi commented 5 years ago

thanks, snp_dict.tsv was updated and could be downloaded and used to yield chrom and local position without changing ways to calling parser

snayfach commented 5 years ago

Thanks - I assume it is 1-indexed rather than 0-indexed. Can you confirm?

zjshi commented 5 years ago

Sorry if it sounds confusing, but they are 0-indexed for both global and local positions.

snayfach commented 5 years ago

Not confusing. Thanks

On Wed, Feb 13, 2019 at 5:10 PM Zhou (Jason) Shi notifications@github.com wrote:

Sorry if it sounds confusing, but they are 0-indexed for both global and local positions.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/zjshi/gt-pro2.0/issues/2#issuecomment-463443022, or mute the thread https://github.com/notifications/unsubscribe-auth/ACAbrRCPNKGSRnDb05me0bfjMuwGdQUhks5vNLdvgaJpZM4a1Wgm .

snayfach commented 5 years ago

1-indexed positions are a bit more standard for public consumption, but works fine for me :)

On Wed, Feb 13, 2019 at 5:10 PM Stephen Nayfach snayfach@gmail.com wrote:

Not confusing. Thanks

On Wed, Feb 13, 2019 at 5:10 PM Zhou (Jason) Shi notifications@github.com wrote:

Sorry if it sounds confusing, but they are 0-indexed for both global and local positions.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/zjshi/gt-pro2.0/issues/2#issuecomment-463443022, or mute the thread https://github.com/notifications/unsubscribe-auth/ACAbrRCPNKGSRnDb05me0bfjMuwGdQUhks5vNLdvgaJpZM4a1Wgm .

zjshi commented 5 years ago

I see, thanks for the point, I will make it clear in documents all positions are 0 indexed. I would also do an assessment when I have more time later to see how costly it is to transform 0 indexed files to 1 indexed ones.