Is it possible to get a subset of VCF file every 10 Mbp across a particular chromosomes

Question

[Hann]

Hello all,

I have a vcf file (SNP data) of 157 a cereal crop individuals. I have extracted only SNPs in chromosome 9 as the following:

vcftools --vcf file.vcf --chr chr09 --recode --recode-INFO-all --out chr9_output

I am interested in getting a subset of VCF files in a window 10 Mbp from chromosome 9 vcf file. Is this possible?

.

Thanks,

[WouterDeCoster]

You want to split your vcf in 10 Mbp windows? Or do you want to extract a certain 10 Mbp window?

[Hann]

I want to have a vcf file has the SNPs from 1 to 10 Mbp another vcf file has SNPs from 10 Mbp to 20 Mbp ... and so on

one of the ideas that I think it will work is use bedtools intersect like this

bedtools intersect -a Fonio_cultivated_noSingletons_chr09A.recode.vcf -bed wind.bed -wo test

wind.bed is a tab-delimited file has one line as following

chr09A   1   1000000

But I am getting error Error: unable to open file or unable to determine types for file Fonio_cultivated_noSingletons_chr09A.recode.vcf

[ATpoint]

That means that your VCF is not formatted properly, maybe the header is missing. Also -bed is the wrong flag, use -b, please read the docs why. Also, tabix will be notably faster. Simply make a file with the windows you want and loop through it with the linked tabix code.

[Hann]

Very good! worked! Thanks a lot!

Answer 1

[ATpoint]

Compress your file with bgzip, then use tabix to index it. From there on you can extract any given interval, e.g. your 10Mb window with a simple command as described here in the manual: http://www.htslib.org/doc/tabix.html#EXAMPLE