Allele Frequency Calculator

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This tool calculates population-wide allele frequencies for variations within a defined chromosomal region.

Name for this job (optional):

Species:

Human

Assembly: GRCh37.p13

Region Lookup:

e.g. 1:1-50000

Choose data collections or provide your own file URLs:

Genotype File URL:

Sample-population file URL: https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/integrated_call_samples_v3.20130502.ALL.panelSample-population file URL: https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/phase1_integrated_calls.20101123.ALL.panelSample-population file URL: https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/integrated_call_male_samples_v3.20130502.ALL.panel

The genotype file should be VCF only.<a href="/info/website/upload/sample_files/Pulmonary_function.vcf.txt" class="popup"> Example VCF file </a>Genotype file URL:

e.g: https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz

Choose whether to apply any filtering to the output.Filters:

No filtering

By individuals

By populations

This file lists all the individuals and the population they come from.<a href="/info/docs/tools/allelefrequency/sample_panel.html" class="popup">Find out more on what a panel file is.</a>Sample-population mapping file URL:

e.g: https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/integrated_call_samples_v3.20130502.ALL.panel

Select one or more phase 3 populations:

Select one or more phase 1 populations:

Select one or more phase 3(male) populations:

Select one or more populations:

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ALL
ACB
ASW
BEB
CDX
CEU
CHB
CHS
CLM
ESN
FIN
GBR
GIH
GWD
IBS
ITU
JPT
KHV
LWK
MSL
MXL
PEL
PJL
PUR
STU
TSI
YRI

ALL
ACB
ASW
BEB
CDX
CEU
CHB
CHS
CLM
ESN
FIN
GBR
GIH
GWD
IBS
ITU
JPT
KHV
LWK
MSL
MXL
PEL
PJL
PUR
STU
TSI
YRI

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Allele Frequency Calculator

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