Closed rmurray2 closed 10 months ago
That is correct. The symbolic star allele <*>
is a placeholder for alleles not observed in the data which allows to represent genotype likelihoods of non-reference genotypes.
See also the VCF specification https://samtools.github.io/hts-specs/VCFv4.3.pdf
I'd like to get the nt count at each position from a bcf file (exactly like this question)
The posted solution is:
bcftools mpileup --annotate FORMAT/AD
. I tried using--annotate
and passing the output tobcftools call
, but I'm not entirely clear about the what the allelic depth field means in the resulting bcf file. Here are a couple of bcf file entries with only the relevant info shown:example 1:
Question 1: Does this mean that the nucleotide counts at this position are G:109; C:1; A:1; T:0 ? Question 2: What does <*> mean?
example 2:
Question 3: Does this mean the nucleotide counts are G:118; C:2; T:1; A:1 ?
Thanks!