Closed j-coll closed 6 years ago
Nice, let's implement the * for now.
Although it shouldn't be a problem, be aware that GATK represents spanning deletions as * https://gatkforums.broadinstitute.org/gatk/discussion/6926/spanning-or-overlapping-deletions-allele
That should be a problem (in theory), @j-coll actually the two options to implement are:
0/*
-> 0/1
, 0/2
, 0/3
... 0/n
*/*
-> 1/1
, 1/2
, 2/2
... 1/*
would be part of */*
Implementing Option C with new genotypes HOM_REF
, HOM_ALT
, HET
, HET_REF
, HET_ALT
and MISS
Genotype filter accepts a list of genotypes per sample. Querying multi-allelic genotypes is not always as easy, because there are multiple combinations that depends on the number of secondary alternates (0/1, 0/2, 1/2, 3/5, ...)
This operation can be pretty easy. Since #192, a list with all the loaded genotypes is stored and updated in the StudyConfiguration.
Option A
We can allow wildcards (
*
) as "any allele different than 0 or missing". Example:0/*
->0/1
,0/2
,0/3
...0/n
1/*
->1/1
,1/2
,1/3
...1/n
*/*
->1/1
,1/2
,2/2
...Option B
An alternative can be accept an
n
instead instead of a wildcard*
but with the same meaning:0/n
n/n
Option C
There is also other alternate to accept genotype aliases, which will help with polyploidy and phased genotypes:
HOM_REF
->0
,0/0
,0/0/0
, ...HOM_ALT
->1
,1/1
,1|1
,2/2
,3/3
,1/1/1
, ...HET
->0/1
,1/2
,0/2
,2/4
,0|1
,1|0
,0/0/1
, ...HET_REF
->0/1
,0/2
,0/3
,0|1
, ...HET_ALT
->1/2
,1/3
,2/4
,2|1
, ...MIS
->.
,./.
,././.
, ...Conclusion
We will go for Option C, as is the most flexible solution
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