POS Length of 1000 genomes VCF

Question

[sebastianvencken]

Fairly new to the whole population genetics field and have what is probably a very simple question: how do I obtain the position (POS) range of each VCF file from the 1000 genomes project (e.g. ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf)? Getting familiar with vcftools so if there is a way to do this with that, that would be great.

Thanks

[Pierre Lindenbaum]

it's not clear to me.

[sebastianvencken]

The 1000genomes VCF files are per chromosome and only have one genomic range. I was hoping to obtain this genomic range (i.e. chr1:min-max)

Answer 1

[Pierre Lindenbaum]

curl -s  "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz" |\
 gunzip -c |\
 awk -F '\t' 'BEGIN{m=250E6;M=0;}/^#/ {next;} {v=int($2);if(v<m) m="v;if(v">M) M=v;} END {printf("%d -> %d\n",m,M);}'


16050075 -> 51244237

or, as the POS are sorted you can simply use:

$ curl -s  "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz" | \
 gunzip -c | grep -v "^#" |\
 cut -f2 | (head -n1;tail -1)
16050075
51244237

[sebastianvencken]

Thanks for the info, however I was wondering if there may be a way without decompressing the VCF by any chance? e.g. by using tabix?

Answer 2

[Mitch Bekritsky]

Using bcftools, you should be able to do something like this without decompressing your VCF:

bcftools query -f "%POS\n" <your VCF> | awk 'NR == 1; END{print}

A word of warning: I haven't tried this out yet, so it might contain an error or two.

[Pierre Lindenbaum]

well, the VCF is decompressed under the hood....