[Vcftools-help] VCFtools calculating SNP density for specific genomic coordinates

[Christina C. <chr...@cs...>]

To whom it may concern,

I am having an issue using the --SNPdensity option for specified bins of
size. My code looks like this:
vcftools --gzvcf
"ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz"
--chr 6 --from-bp 31783291 --to-bp 31785717 --SNPdensity 2426 --out genename

I should receive only one output (that is the snp density for the specified
genomic coordinates/gene) but I am receiving snp densities in the
out.snpden file, the bin size matches the bp end to the bp start so I'm not
sure what else could be the problem. I have looked online for answers but
was not able to find anything. Any suggestions or help would be much
appreciated. Thank you.

Sincerely,
Christina Chavez
Department of Biological Science
California State University, Fullerton
chr...@cs...