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