Justin Paschall

install prob ga4gh_repo add-referenceset

2

I'm trying to follow the instructions here: http://ga4gh-reference-implementation.readthedocs.io/en/latest/demo.html and am getting the error below ``` $ ga4gh_repo add-referenceset registry.db hs37d5.fa.gz -d "NCBI37 assembly of the human genome" --species '{"id": "9606",...

Per position allele count reporting utility ( like bam-readcount)

5

Looking for general comments about utility and approach - not ready for final review yet. This PR adds functionality to produce a per-position report of counts of reads reporting an...

Hi @fnothaft - I'd like to demonstrate joint calling of genotypes using Avocado for a specific genomics regions using the bin "hive-style" partitioned data. Input: 1) gVCF files for 10+...

Benchmark against Precision FDA or other "truth-sets"

1

It will be useful to benchmark Avocado against some truth sets such as: https://precision.fda.gov/challenges/truth This should give use some false-neg false-pos, precision/sensitivity measures. Do we have an existing pipeline /...