Question: Extract allele count from gnomAD using R
4
gravatar for Nicolas Rosewick
15 months ago by
Belgium, Brussels
Nicolas Rosewick8.8k wrote:

Hi,

Is there a way to extract the allele count for each population of a specific variant using R (oar maybe through a REST API but I couldn't find one for gnomAD..)

For instance I would like to have these informations e.g. for variant https://gnomad.broadinstitute.org/variant/1-55516888-G-GA . I'm interested in the column "Alle Count" and "Allele number".

Thanks

enter image description here

gnomad R • 1.2k views
ADD COMMENTlink modified 15 months ago by zx87549.3k • written 15 months ago by Nicolas Rosewick8.8k

Not API, but maybe this bioconductor package - MafDb.gnomAD.r2.0.1.GRCh38 ?

Or we can always try and scrape the table, maybe see rvest.

ADD REPLYlink modified 15 months ago • written 15 months ago by zx87549.3k

Related post: Extract gnomad AF for specific position with R

ADD REPLYlink written 15 months ago by zx87549.3k

varsome has an API, it needs a login, and might not be free.

ADD REPLYlink written 15 months ago by zx87549.3k

Is tabix helpful? get in VCF format and use bcftools to extract fields of interest as tsv.

tabix "ftp://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_genotype/gnomad.genomes.r2.0.1.sites.GRCh38.noVEP.vcf.gz" "1:55051215-55051216"

1   55051215    rs778104784 G   GA  82149.1 PASS    AC=159;AF=5.13998e-03;AN=30934;AC_AFR=156;AC_AMR=0;AC_ASJ=0;AC_EAS=0;AC_FIN=0;AC_NFE=1;AC_OTH=2;AC_Male=91;AC_Female=68;AN_AFR=8716;AN_AMR=838;AN_ASJ=302;AN_EAS=1622;AN_FIN=3494;AN_NFE=14980;AN_OTH=982;AN_Male=17104;AN_Female=13830;AF_AFR=1.78981e-02;AF_AMR=0.00000e+00;AF_ASJ=0.00000e+00;AF_EAS=0.00000e+00;AF_FIN=0.00000e+00;AF_NFE=6.67557e-05;AF_OTH=2.03666e-03;AF_Male=5.32039e-03;AF_Female=4.91685e-03;GC_AFR=4202,156,0;GC_AMR=419,0,0;GC_ASJ=151,0,0;GC_EAS=811,0,0;GC_FIN=1747,0,0;GC_NFE=7489,1,0;GC_OTH=489,2,0;GC_Male=8461,91,0;GC_Female=6847,68,0;AC_raw=159;AN_raw=30992;AF_raw=5.13036e-03;GC_raw=15337,159,0;GC=15308,159,0;AC_POPMAX=156;AN_POPMAX=8716;AF_POPMAX=1.78981e-02
1   55051216    rs117258312 G   A   6193.45 PASS    AC=19;AF=6.20347e-04;AN=30628;AC_AFR=0;AC_AMR=0;AC_ASJ=0;AC_EAS=18;AC_FIN=0;AC_NFE=1;AC_OTH=0;AC_Male=11;AC_Female=8;AN_AFR=8410;AN_AMR=838;AN_ASJ=302;AN_EAS=1622;AN_FIN=3494;AN_NFE=14984;AN_OTH=978;AN_Male=16926;AN_Female=13702;AF_AFR=0.00000e+00;AF_AMR=0.00000e+00;AF_ASJ=0.00000e+00;AF_EAS=1.10974e-02;AF_FIN=0.00000e+00;AF_NFE=6.67379e-05;AF_OTH=0.00000e+00;AF_Male=6.49888e-04;AF_Female=5.83856e-04;GC_AFR=4205,0,0;GC_AMR=419,0,0;GC_ASJ=151,0,0;GC_EAS=793,18,0;GC_FIN=1747,0,0;GC_NFE=7491,1,0;GC_OTH=489,0,0;GC_Male=8452,11,0;GC_Female=6843,8,0;AC_raw=19;AN_raw=30856;AF_raw=6.15764e-04;GC_raw=15409,19,0;GC=15295,19,0;AC_POPMAX=18;AN_POPMAX=1622;AF_POPMAX=1.10974e-02

output from GNOMAD vcf is huge (source : https://storage.googleapis.com/gnomad-public/release/2.1.1/vcf/exomes/gnomad.exomes.r2.1.1.sites.vcf.bgz)

ADD REPLYlink modified 15 months ago • written 15 months ago by cpad011213k
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