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kantorlab / hivmmer

Alignment and variant-calling pipeline for Illumina HIV sequences.
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support for Gag? #5

Closed drescs closed 4 years ago

drescs commented 5 years ago

I noticed that there is no option to specify "gag" as the region. I made my own reference (thanks for the help with that) for gag but seems a region must be specified from pol, int, or env. It looks like maybe this is only used for noting what gene a codon is in--if that is the case, can I just use int as the region, or is there more going on here? Or can I change the code to add "gag" as an option for the reference?

Thank you! Sara

mhowison commented 5 years ago

Hi Sara, sorry for the delay in responding to you on this, but I wanted to let you know that support for gag (and in fact the whole HIV genome) is planned for version 0.2.0 of hivmmer. I will send you an update when that version is released.

drescs commented 5 years ago

Thank you Mark. I actually was able to get a fairly good workaround by creating my own gag reference but setting the fragment to "int." In fact for my application I am setting the fragment to int for my pol sequences as well, so that I get all AA positions in the variants file, rather than just those relevant to drug resistance. It seems to be working well!

On Fri, Oct 18, 2019 at 11:10 AM Mark Howison notifications@github.com wrote:

Hi Sara, sorry for the delay in responding to you on this, but I wanted to let you know that support for gag (and in fact the whole HIV genome) is planned for version 0.2.0 of hivmmer. I will send you an update when that version is released.

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