Question: vcf files: counting number of variants in genomic windows of chosen size
0
gravatar for spiral01
10 months ago by
spiral0170
spiral0170 wrote:

Is there a tool to count the number of variants in each genomic window of user-designated size? Something that would work along the lines of vcftools --TajimaD which takes as argument the size of the window you would like and then calculates Tajima's D in each window. I would like to simply count the number of variants in each window.

snp • 658 views
ADD COMMENTlink modified 10 months ago by Alex Reynolds26k • written 10 months ago by spiral0170
2
gravatar for harold.smith.tarheel
10 months ago by
United States
harold.smith.tarheel4.2k wrote:

See Plotting SNP density along a chromosome from VCF files

ADD COMMENTlink written 10 months ago by harold.smith.tarheel4.2k

Apologies for the repeat question. That is exactly what i was after. Thank you.

ADD REPLYlink written 10 months ago by spiral0170
0
gravatar for Alex Reynolds
10 months ago by
Alex Reynolds26k
Seattle, WA USA
Alex Reynolds26k wrote:

Via BEDOPS:

$ bedmap --echo --count genes.bed <(vcf2bed < variants.vcf) > answer.bed

If your genes are in another format, say GFF:

$ bedmap --echo --count <(gff2bed < genes.gff) <(vcf2bed < variants.vcf) > answer.bed

If you have generic windows, replace genes.bed with a windows.bed of your design.

ADD COMMENTlink modified 10 months ago • written 10 months ago by Alex Reynolds26k

Hi, I am getting segmentation fault: 11 when using the first bedmap command as such:

bedmap --echo --count windows.bed <(vcf2bed < chr21.vcf.gz) > chr21.coverage.txt

The final output keeps giving me a count of 0 for each window. I'm not sure how to interpret this?

ADD REPLYlink written 10 months ago by spiral0170

The file chr21.vcf.gz is not a VCF file, but is instead a gzip-compressed binary. Extract it and then pipe the extracted data to vcf2bed, e.g.:

$ bedmap --echo --count --delim '\t' windows.bed <(gunzip -c chr21.vcf.gz | vcf2bed -) > windows_with_counts_of_variants.bed

Interpretation: If some of your windows are not on chr21, and all the variants in chr21.vcf are from chr21, then expect zero-counts over those windows which are not on that chromosome.

ADD REPLYlink modified 10 months ago • written 10 months ago by Alex Reynolds26k
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