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Illumina / strelka

Strelka2 germline and somatic small variant caller
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can strelka2 export variants in halplotype form? #29

Open ShannonDaddy opened 6 years ago

ShannonDaddy commented 6 years ago

Hi, strelka team

I was really impressed by the model and performance of strelka in calling somatic mutations. But I have a question on the variant form in the vcf file. Can strelka report MNPs, complex variants such as: --MNP-- chr1 100 AG GC --Complex-- chr7 200 TTTCA AT

Thanks!

ctsa commented 6 years ago

The answer to this question is in flux: We've already implemented a haplotype model for the germline caller already, so the germline variants are phased such that MNVs and complex alleles can be inferred from the primitive alleles and phasing information.

For the somatic caller, we are in the process of setting up a haplotype model which would supply similar phasing information. This is promising but a bit trickier than the germline case. For now, the noise filtration parameters for the somatic caller are designed to allow for the common occurrence of MNVs in cancer samples, but the corresponding SNVs will appear together in the somatic calling output without any phasing details.

Lies-VO commented 1 year ago

Hi Strelka team,

Do you have an update on the haplotype model for the somatic caller? This would be a really nice feature.

Thanks!