Read genotype information with VariantAnnotation

Question

[jeni]

Hi,

is there any way to read genotype information (FORMAT field) GT:AD:AF using VariantAnnotation? Moreover, as I have used a somatic caller, I have 2 format fields for each variant (one from normal and one from tumour sample); so, how can I preserve sample name as a column name when I transform this vcf to a dataframe?

As an example:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  Normal_sample   Tumour_sample
1   52052   .   C   T   .   PASS    CONTQ=93;DP=56 GT:AD:AF 0/0:36,0:0.026  0/1:15,4:0.238

I am reading the vcf with this command:

as.data.frame(cbind(vcf@rowRanges@seqnames,vcf@rowRanges@ranges@start, vcf@fixed, info(vcf)))

So I get the following dataframe:

vcf.rowRanges.ranges.start  REF ALT QUAL    FILTER  CONTQ   DP  
52052    C    T  pass 93   56

I would like to get something like this:

vcf.rowRanges.ranges.start REF ALT QUAL FILTER CONTQ DP NGT NAD NAF TGT TAD TAF
52052    C    T  pass 93   56  0/0  36,0 0.026  0/1 15,4:0 0.238

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

Answer 1

[benformatics]

This is pretty well illustrated in the manual... Most standard entries can be accessed using the info() or geno() function call. I don't think you are going to be able to simply cbind all this information together without checking the format of each of the different columns you want to append. For instance AD provides two values - so you would likely have to make separate data.frames before merging.

> your.vcf <- readVcf('your.vcf')
> geno(your.vcf)
List of length 5
names(5): GT AD DP GQ PL
> head(geno(your.vcf)$GT)[[1]]
[1] "0/1"
> geno(your.vcf)$AD[[1]]
[1] 10  2
> info(your.vcf)$AF[[1]]
[1] 0.5