Matt Shirley

icon indicating a website link http://mattshirley.com icon indicating an email [email protected]

icon company @novartis icon location Boston, MA icon location Data Scientist @Novartis, CSO Sturge-Weber Foundation. Oncology and Rare Disease Research [email protected]

Results 43 issues of Matt Shirley

Tagged release

I'm interested in trying out shoal, and would integrate it into our pipeline, but it would be nice to have a tagged release instead of pointing at a specific commit....

Missing test data

14 comment

I noticed that there is not test data containing a full Minion run. Could you please fix this?

Fingerprint SNP positions should be hg38 coordinates, not GRCh37

- Need to edit the VCF header: https://github.com/Novartis/pisces/blob/master/pisces/scripts/kmer_counts_to_fingerprint_strand_and_pcthuman.py#L173-L206 - Liftover the positions in the 4th column of https://github.com/Novartis/pisces/blob/master/pisces/data/fp_kmers.txt