Extract gnomad AF for specific position and REF/ALT allele with R
0
4
Entering edit mode
3.2 years ago

Hi,

I've a list of genomic position and ref / alt allele such as :

# A tibble: 10 x 4
   chrom       pos ref   alt  
   <chr>     <int> <chr> <chr>
 1 1      16953672 C     T    
 2 2      96971401 A     G    
 3 2     211421264 G     A    
 4 5      55298397 A     G    
 5 10    104235799 G     GT   
 6 11       784219 T     C    
 7 19     55671382 C     T    
 8 X     142804304 A     AT   
 9 10     88615391 A     T    
10 19     15789302 T     C

I installed the MafDb.gnomAD.r2.1.hs37d5 package to annotate these positions.

https://bioconductor.org/packages/release/data/annotation/html/MafDb.gnomAD.r2.1.hs37d5.html

However when I want to specify the ref and alt allele in the gscores request I've a warning :

mafdb <- MafDb.gnomAD.r2.1.hs37d5
gscores(mafdb, GRanges("1:569474"),ref="A",alt="T")
GRanges object with 1 range and 1 metadata column:
      seqnames    ranges strand |        AF
         <Rle> <IRanges>  <Rle> | <numeric>
  [1]        1    569474      * |     6e-04
  -------
  seqinfo: 1 sequence from hs37d5 genome; no seqlengths
Warning message:
In .scores_snrs(x, ranges, pop, summaryFun, quantized, scores.only,  :
  arguments 'ref' and 'alt' are given but there is only one score per genomic position.

However some positions in gnomad may have different ref / alt allele (but same chrom and pos). For instance :

https://gnomad.broadinstitute.org/variant/4-106155467-G-A and https://gnomad.broadinstitute.org/variant/4-106155467-G-C that have respectively 0.00003548 and 0.000003993 of allele frequency in the general population.

How can I specify ref and alt to have the correct AF ?

Thanks

R gnomad af allele frequency annotation • 1.8k views
ADD COMMENT

Login before adding your answer.

Traffic: 2187 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6