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Same position, multiple alt alleles, no depth info - Why ?
Sorry for the simplistic question, but I am new at this.
Using Mutect2 (and a few other callers) to look for somatic variants,
we are getting multiple cases where several alt alleles are identified
at the same position (on same single line in VCF).
When we try extracting info from VCF (through Gemini database),
we can't get any additional info for those variants with multiple alt alleles at same position.
In the VCF, I can't see any allele depth.
Why are we getting a single entry for both alt alleles ?
How can we correct our VCF so we can see how many reads
we have for each alt allele at this same position ?
Sorry, I'm just running out of time to solve it.
Let me know where I can find info on this.