Question: Tollaly confused about finding variants allel frequencies.
3
gravatar for amir.jebelli
3.6 years ago by
amir.jebelli50
Iran/Mashhad
amir.jebelli50 wrote:

Hi,

I checked a few variant allele frequencies but I got different result from different websites.
I checked my variances in NHLBI Exome Sequencing Project (ESP)
http://evs.gs.washington.edu/EVS/
and also check with this site http://db.systemsbiology.net/kaviar/ from System Biology.

for example for the following variance I got MAF = 0.43 from ESP and MAF < 0.01 from Kaviar !

Can anybody tell me the popular and academic accepted way of reporting allele frequency in papers ?

maf • 1.6k views
ADD COMMENTlink modified 3.6 years ago by Cyriac Kandoth5.2k • written 3.6 years ago by amir.jebelli50
2
gravatar for Cyriac Kandoth
3.6 years ago by
Cyriac Kandoth5.2k
Memorial Sloan Kettering, New York, USA
Cyriac Kandoth5.2k wrote:

You can run your variants through Ensembl's VEP, which reports the following columns (as of VEP v81)

GMAF - Non-reference allele and frequency of existing variant in 1000 Genomes
AFR_MAF - Non-reference allele and frequency of existing variant in 1000 Genomes combined African population
AMR_MAF - Non-reference allele and frequency of existing variant in 1000 Genomes combined American population
ASN_MAF - Non-reference allele and frequency of existing variant in 1000 Genomes combined Asian population
EAS_MAF - Non-reference allele and frequency of existing variant in 1000 Genomes combined East Asian population
EUR_MAF - Non-reference allele and frequency of existing variant in 1000 Genomes combined European population
SAS_MAF - Non-reference allele and frequency of existing variant in 1000 Genomes combined South Asian population
AA_MAF - Non-reference allele and frequency of existing variant in NHLBI-ESP African American population
EA_MAF - Non-reference allele and frequency of existing variant in NHLBI-ESP European American population

 

ADD COMMENTlink written 3.6 years ago by Cyriac Kandoth5.2k

Hi, Cyriac

I checked My variants in ensemble but all MAF fields are filled with - unfortunately no value reported there. you can see my result here on ensemble.

ADD REPLYlink written 3.6 years ago by amir.jebelli50
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