Remove CNVkit and Sequenza gene tables

[hsienchao]

No description provided.

[hsienchao]

The CNVkit and Sequenza data flow is being improved. The old way is to upload the CNV segment data and then join the gene table. This is very slow. These two tables need around 30 mins to refresh the joined tables. Now I plan to improve this by creating the join table first by bedtools' intersect and groupy commands. Then we upload the segment file with gene list.

[hsienchao]

Tried to use Manoj's Sequenza gene level script to process the old cases. I found this script generates inconsistent CN and A/B values. For example:

So I made a script which will use the segment that has highest overlapped regions with the gene. I've re-processed all old cases on Frederick server.

#chromosome	start.pos	end.pos	Gene	CNt	A	B
chr1	13424002	13648656	PRAMEF15	2	1	0
chr1	13448049	13671691	PRAMEF13	2	1	0
chr1	13448049	13671691	PRAMEF14	2	1	0
chr1	13474688	13698358	PRAMEF19	2	1	0
chr1	13495283	13718962	PRAMEF17	2	1	0
chr1	13521972	13747733	PRAMEF20	2	1	0
chr11	48346492	48347482	OR4C3	2	2	1
chr14	106518399	106518853	IGHV3-7	2	1	0
chr18	3499182	3880068	DLGAP1	2	2	1
chr5	128796102	129072911	ADAMTS19	2	2	1