1000Genomes To Haploview

Question

[Guilherme]

Good Morning,

My name is Guilherme and first off all I would like to leave here my excuses for the possible dumb question, because I'm relative new in the Bioinfo. area…..so here's my question...... I would like to know if there is a way to convert the VCF files (I got sequences of a region of interest of Chromossome 6 from the FTP download website of the 1000Genome), to Haploview files, so I can work with the Haploview program. Actually I'm wondering if there is a way to get the 1000Genome sequences directly with the Haploview program like the program does with the HapMap Project website. I'm not familiar with the VCFtools / tabix …. and I just used these programs to get the sequences from the FTP.

Thanks,

Guilherme

[Laura]

This is indeed correct.

We are looking at adding the filtering to the VCF to PED tool but as we are in the process of moving architectures, it isn't clear when that will happen

Answer 1

[Caddymob]

You sure can! You need vcftools, tabix, and plink. Here is how it would look, you need to define the chromosome $CHR and region $REGION below.

tabix -fh ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20110521/ALL.chr$CHR.phase1_integrated_calls.20101123.snps_indels_svs.genotypes.vcf.gz $REGION > ALL.chr$CHR.phase1_integrated_calls.20101123.$REGION.vcf
vcftools --vcf ALL.chr$CHR.phase1_integrated_calls.20101123.$REGION.vcf --plink-tped --out 1000G_integrated_calls.20101123.$REGION
plink --tfile 1000G_integrated_calls.20101123.$REGION --recodeHV --out 1000G_integrated_calls.20101123.$REGION.ForHaploview

The plink --recodeHV option makes a text-based PED and a .info file that Haploview will read. I've found with vcftools the transposed ped file (--plink-tped) is the only way to gt big regions to work, otherwise vcftools crashes because of memory errors.

[Guilherme]

Both answers fixed my problem!! Thank you very much caddymob!!! Guilherme

Answer 2

[Laura]

We now have a tool which will generate the necessary input files for haploview

http://browser.1000genomes.org/Homo_sapiens/UserData/Haploview

http://www.1000genomes.org/vcf-ped-converter

Please note that at very large numbers of individuals or variants haploview gui tends not to scale

[Guilherme]

Both answers fixed my problem!! Thank you very much Laura!!!

Guilherme

[Jimbo]

I know this is rather old now.

But just to note that as the 1000 genomes file includes > biallelic markers, it means the file can't be loaded into haploview... You'll need to add an extra step to remove such markers.