Question: Haplotype Frequency Of A Range From 1000 Genomes Data Using Tabix And Other Utils
1
gravatar for jvijai
6.6 years ago by
jvijai10
jvijai10 wrote:

Aim: Download public data in a range, calculate the frequency of haplotypes in that region for overall and each ethnic population.

I want to download the region around BRCA1 from the 1000genomes data.

tabix -fh http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/ALL.chr17.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz 17:41,196,312-41,277,340 >BRCA1_1000g_20101123.vcf

So I have my BRCA1 genotype data and I want to check the frequency just as a QC measure.

vcftools --gzvcf BRCA1_1000g_20101123.vcf.gz \
    --freq \
    --out BRCA1Copy_1000g_20101123.vcf.freq

Now, I want to now find the common and "all" haplotype blocks and the frequency of haplotypes in this region.
What filters should be applied on allele frequencies . Any help is very much appreciated.

tabix haplotype plink haploview • 2.1k views
ADD COMMENTlink modified 6.6 years ago • written 6.6 years ago by jvijai10

Can you make an example of the output that you would expect to see? Do you want the frequency of all the possible haplotypes, or only of the ancestral alleles haplotypes?

ADD REPLYlink written 6.6 years ago by Giovanni M Dall'Olio26k
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