reverse compliment about snpgenie

[singing-scientist]

Greetings, @harpur ! Thanks for using SNPGenie, and apologies for the trouble. I have received the example data. Could you now please provide the exact command-line arguments used, so that I may replicate and diagnose the problem? Many thanks.

[harpur]

Sure thing
First the forward direction (which also outputs stats for the negative):
snpgenie.pl --minfreq=0.01 --snpreport=NC_037638.1.S.AFAN.vcf --vcfformat=1 --fastafile=_NC_037638.fasta --gtffile=NC_037638.1.gtf --outdir NC_037638

and then the negative direction (which should throw the error above):
vcf2revcom.pl _NC_037638.fasta NC_037638.1.gtf NC_037638.1.S.AFAN.vcf

[singing-scientist]

Thanks very much for your patience during this troubling time.

First, I tried the snpgenie command and it appears to me to run correctly — although I quit after an hour since this was obviously an example not meant for my laptop. Keep in mind that, as described in the documentation, there must only be one transcript per unique gene id.

Second, vcf2revcom.pl, please trying using the script available at this (snpgenie) repository, NOT the EBT repository. As described in the documentation, you should be able to run the following, where 27754200 is the length of your sequence:

vcf2revcom.pl NC_037638.1.S.AFAN.vcf 27754200

Please let me know if that works as expected!

I apologize for the "hack-iness" of these solutions, as SNPGenie was originally written for single-stranded RNA viruses, and this is all I've had time to implement so far. I hope to write an entirely new version in Python in the future, but that's some time away!

[singing-scientist]

Also, given a quick pass I was not able to find any antisense (-) product results when running for the sense (+) -- indeed, those should not occur. If you could provide any specific examples of antisense product results that are being reported, I'd be glad to look into it.

[harpur]

Hey Chase, thanks for your response. I pulled the repo and re-ran everything. It worked correctly. I think we must've pulled an older version that was throwing errors at us. I am happy to close this issue. Thanks for your help. Stay safe!

[singing-scientist]

So glad this worked out! Please don't hesitate to raise any subsequent questions and I'll do my best to get back promptly. Wishing you and yours stay safe and well!