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SelectVariants - Information from absent alleles
I have a problem using SelectVariants at multiallelic sites. For a given patient (let's call him P1) I want to keep only the positions which are variant in his genome. I use the following options :
--preserveAlleles : I keep the original form of the alleles, as they are called in the original vcf
--excludeNonVariants : I do not want 0/0 positions for the patient P1
--removeUnusedAlternates : I want only the alleles which are specific to P1
The last point is the problematic one. Yes, it partially work. For example, let's say I have this variant in the original VCF, with two alleles in my population :
chrZ 375987 . TA T,TAA
In the P1-only-VCF, after extraction, I only have (let's say that P1 is 0/1) :
chrZ 375987 . TA T
Which is correct.
Nevertheless, even if only the good allele is kept, all the information from the INFO fields is preserved (for all the alleles) .
A little sample from the ANN records of the P1-only-file :
I put in bold the information from an allele absent in P1. This is annoying because it disturb the interpretation. If anybody have a suggestion, it will be the very welcomed !
Thanks by advance,