Arun Ahuja
Arun Ahuja
@timodonnell What are thinking for this? Two things I could see are 1) having a github repo that has an example that is cloneable or 2) a maven archetype? I...
We could even support a cross-language serialization format
This can be resolved with `--trim-ranges` but I think that should be the default then? Otherwise, I'm not sure how `TakeLociIterator` differentiates between empty loci and excluded loci.
I could see the advantage of having the reads at the pileup as well since there is a difference between no reads mapped to that region or all the reads...
Related references: 1. Rimmer, A. et al. Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications. Nat. Genet. 1–9 (2014). doi:10.1038/ng.3036 2. Rizk, G., Gouin, A.,...
We've a developed a lot of this through the TCGA poster. I'm assembling a set of reads around ~100 variants that we can use as calibration using forward.
We can do this if we are loading ADAM reads or some other parquet serialized data. Thoughts are on our approach to this @ryan-williams @timodonnell
Both of those are private buckets. The DREAM data is available in a public bucket at `gs://public-dream-data/`
I've seen this as well with ensembl85 in `varcode`. @iskandr mentioned in the latest pyensembl, but we need to upgrade to the new `varcode` and `pyensembl` interfaces in `cohorts`. I've...
Closed by @jburos work in #147?