Tiffany Delhomme
Tiffany Delhomme
that works for me! see [here](https://help.github.com/articles/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent/) for detailed steps to add ssh key
Hi, I am also interested in this particular statistic, in my case when I consider that ```Probability of incorrect variant call P = 10 ^ (-SomaticEVS/10)``` it seems that P...
Note: I think it is not "truncated" but more re-scaled, i.e. ``` if TumorSampleAltAlleleFraction > 0.5 then TumorSampleAltAlleleFraction = 0.5 ```
I found [this piece of code]( https://github.com/Illumina/strelka/blob/ac7233f1a35d0e4405848a4fc80260a10248f989/src/c%2B%2B/lib/applications/strelka/position_somatic_snv_strand_grid_vcf.cpp#L136-L140) which re-scales the AF to prevent for LOH regions. Does this have an influence on the interpretation of the final EVS score? See...
I also noted this unexpected behaviour!
What about MAF ([minor allele frequency](https://en.wikipedia.org/wiki/Minor_allele_frequency)) instead of allele frequency?
Yes I like also VAF for individual allelic fraction.
VF for variant frequency?
Does GATK not respect the VCF specification? https://gatkforums.broadinstitute.org/gatk/discussion/6202/vcf-file-and-allele-frequency
This is actually an `htslib` 8yo bug reported [here](https://github.com/samtools/samtools/issues/842), for the moment we should adapt our `mpileup2readcounts` until they correct this.