Extract allele count from gnomAD using R

Question

[Nicolas Rosewick]

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

[zx8754]

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.

[zx8754]

Related post: Extract gnomad AF for specific position with R

[zx8754]

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

• https://api.varsome.com/lookup/1:55516888:G:GA/1019?add-all-data=1&add-ACMG-annotation=1

[cpad0112]

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)