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genotypeType for genotypes with multiple OtherAlt alleles? #897
What should the
Take for instance the following abbreviated VCF record which has a multi-allelic variant for 4
More than two alternative alleles won't happen that often for a snp but will happen often for mnp's and indels.
If I understand the Adam genotype schema correctly then this would lead to 12 genotype parquet records. One record for each combination of alternative allele and sample.
The first set of genotype / parquet record for each sample would have the following allele combinations for each sample.
But how can I determine the correct
Is this correct? Or is there a way to determine if the
I am trying to write a replacement for the
Thanks for describing this!
referenced this issue
Dec 24, 2015
This was meant to be resolved by b1fce67, but was not. I am still having an issue when loading in multi-allelic variants. Here is an example line I am having issue with:
Here is the Stacktrace:
This was closed to track #577, which was closed by the commit referenced above.
For the VCF parse error, I simply added an allele to an existing line, but I now know you cannot do that.
I am trying to figure out how ADAM handles multi-allelic variants.
I also tried to use the VCF spec example and that failed:
I'll go ahead and close this issue.