Allele Frequency Calculator

Question

[786]

Hi I'm using 1000 genome browser and want to retrieve data related to Allele frequency using Allele Frequency Calculator. When I entered chromosome and gene position and after selecting population I get error and it said...

Error:Please provide VCF file, Sample-Population Mapping file and Chromosomal region.

Now what should I do or anyone can guide me that how to use Allele Frequency Calculator plz??

Answer 1

[Zev.Kronenberg]

Here is one way to do it, using vcflib ( https://github.com/vcflib/vcflib)

popStats

INFO: help
INFO: description:
      General population genetic statistics for each SNP

Output : 9 columns :
     1. seqid
     2. position
     3. target allele frequency
     4. expected heterozygosity
     5. observed heterozygosity
     6. number of hets
     7. number of homozygous ref
     8. number of homozygous alt
     9. target Fis
INFO: usage:  popStat --type PL --target 0,1,2,3,4,5,6,7 --file my.vcf

INFO: required: t,target     -- a zero based comma separated list of target individuals corresponding to VCF columns
INFO: required: f,file       -- proper formatted VCF
INFO: required, y,type       -- genotype likelihood format; genotype : GL,PL,GP
INFO: optional, r,region     -- a tabix compliant region : chr1:1-1000 or chr1