SNP/kb in chromosome wise

Question

[adarsh]

Hi,

I need to calculate the SNPs per kb for my rice samples. I have separated out SNPs from the main vcf file as a separate vcf.

Previously I have generated SNP density plot using CMPlot R Package, where I have given 1 Mb window size (10e6). This was able to give the number SNPs per Mb for each chromosome. However when I tried the same tool for my current analysis (SNPs per 1Kb), it is not working, as it is not creating 1 Kb windows as intended.

What could be the possible reason? Is there any alternate method to get this SNPs per Kb and then generate an SNP density plot like the one generated using CMPlot?

Please help

Thanks

Answer 1

[Pierre Lindenbaum]

number of variants per 1Mb, assuming the vcf is ordered on chrom/pos:

bedtools makewindows  -g ref.fasta.fai -w 1000000 | LC_ALL=C sort -t $'\t' -k1,1 -k2,2n | bedtools intersect -a - -b in.vcf.gz  -c  -sorted