Hi all,
How does the VCF output handles multiple ALT alleles ? Some tutorials I
read say that:
ALT the alternate allele expressed as a sequence of one or more A/C/G/T
nucleotides (e.g. "A" or "AAC"). If there is more than one alternate
alleles, the field should be a comma-separated list of alternate alleles.
The most common format subfield is GT (genotype) data. If the GT subfield
is present, it must be the first subfield. In the sample data, genotype
alleles are numeric: the REF allele is 0, the first ALT allele is 1, and so
on.
However, the GT fields in my results only have 0 and 1, even in the
multi-ALTs cases. How can I distinguish between the ALT alleles ?
One example:
supercontig_0 762229 . A G,T 123 .
DP=6;VDB=0.0045;AF1=1;AC1=4;DP4=0,0,3,3;MQ=42;FQ=-35.6 GT:PL:DP:SP:GQ
1/1:62,6,0,62,6,62:2:0:15 1/1:101,14,5,93,0,90:4:0:18
I compared two individuals with a reference genome. I would expect at
least one number 2 in the last two columns.
Best,
Thiago
--
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Thiago Motta Venancio, M.Sc., PhD
http://venancio.openwetware.org/
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