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chasewnelson / SNPGenie

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
GNU General Public License v3.0
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All classified as synonymous #63

Closed marotbone closed 2 years ago

marotbone commented 2 years ago

Hi,

I'm using SNPGenie on bacterial data of pooled samples with very low frequent SNPs which I called with lofreq.

I am using SNPGenie Version: 2019.10.31 with the following command: snpgenie.pl --fastafile=PsymA.fasta --gtffile PsymA_cds.gtf --snpreport PsymA_recode.vcf --vcfformat=2

In my opinion this seems to be the most appropriate option for my case. All works fine so far, but when I check site_results.txt all the sites are classified as synonymous and some columns seem to be missing (e.g ref_nt and codon).

Here is a ZIP file with the input files and the generated output folder. PsymA_test.zip

What could be the reason for this?

Thanks.

Best, Maro

singing-scientist commented 2 years ago

Greetings, Maro!

Thanks very much for using SNPGenie and for the question. Looking at your sites_results.txt file, indeed it is odd. I ran the data for myself, and the site_results.txt looks correct (or at least, not odd):

SNPGenie_Results_CWN.zip

It is possible (likely) this is a bug from an older version. Can you download the latest SNPGenie from this repository and try it again?

Let me know! Chase

marotbone commented 2 years ago

Hi Chase,

Thanks for the support. The strange behavior was caused by the equal sign in the command to pass the fastafile. I am sorry for wasting your time.

Great tool, it seems to perfectly match our needs. Thank you!

Best, Maro

singing-scientist commented 2 years ago

How odd! I'm glad the solution was simple. Please let me know if anything else comes up!

Many thanks, Chase