singing-scientist
commented
5 years ago Hello, @binshuangli !
That is exactly right. What is important is that the SITE COORDINATES (1-based) in the GTF and VCF files match the (1-based) positions in the FASTA file. You can think of SNPGenie input as a single unit corresponding to a single DNA sequence. You will need to run SNPGenie once for every sequence/VCF/GTF combination — be it a genome, chromosome, or scaffold. Thus, in your case, you could place the three input files for each scaffold in its own directory, running SNPGenie once in each directory. Sites and differences can then be summed for genome-wide values, if you wish.
SNPGenie worked for me using your example, using the following command:
snpgenie.pl --vcfformat=3 --snpreport=pool_FR_alfalfa.sorted.utg000001l_pilon10.vcf --fastafile=racon4_pilon10_utg000001l_pilon10.fasta --gtffile=utg000001l_pilon10_corrected_0start.gtf
You should obtain πN = 0.011 and πS = 0.
If that does not work, please provide the exact command-line input you used. Let me know...
Yours, Chase
binshuangli
Hi Chase,
I am working with a genome with multiple scaffolds. I followed the instruction to split the fasta file into individual single sequence fasta file now. I am curious what the next step is. Should I also split the gtf file and vcf file into separate files or they can be left unchanged?
I tried to grep the information from the gtf and vcf file for a specific scaffold. SNPGenie seems to be running OK and then killed displaying "Performing final calculations, noncoding overlap analysis, and output... Killed" for unknown reason. I have the test files attached here: https://drive.google.com/open?id=1HphfXSw7QPJRuXTGf1nO98Cjd_agP6ok