Uma Paila

I encountered the same issue. It issues the "ValueError: Wildcard filter should consist of 4 elements" Also #868 is the same issue. Uma

Adding a comment on this error: The gene tables use GRCh37 build of the genome for which the HGNC mapping for the ensembl gene id "ENSG00000093072" is CECR1. The latest...

I like Brent's idea of '--use-canonical' flag for those who want ranking based on canonical transcripts. The default can still remain the same.

Yes there's a '--canonical' flag in VEP and that should be available in INFO. Not sure about snpEff though.


Hi Gavin, Above is a chr10 plot for ploidy=2, cluster 1 for which normal contamination was 0.99 -Uma

Hi Gavin, The rest of the chromosomes look similar except for chr17 which has an event. Below is the figure. However, ploidy=2, cluster=5 has a normal estimate of 0.91 for...

It is 0.99 for ploidy=2, cluster01 (for fixed cluster size =1) & 0.91 for ploidy=2, cluster05 (for fixed cluster size = 5)

I mailed you the RData.

Running copyCat version 1.6.12, I have a similar error and my VCF has the DP and AF fields. Any suggestions?