gaow
Here I compare size of the VCF input data and the genotype database generated: ``` [GW] ll *.vcf.gz -rw-rw-r-- 1 gaow gaow 977K Mar 22 11:27 YRI.exon.2010_03.genotypes.vcf.gz -rw-rw-r-- 1 gaow...
Currently in my project folder I see: ``` [GW] ll *.DB -rw-r--r-- 1 gaow gaow 0 Mar 22 11:34 VATDemo_genotype.DB [GW] ll *.h5 -rw-rw-r-- 1 gaow gaow 3.1M Mar 22...
The error message looks quite verbose now:  I think previously we only see that read line at default verbosity?
Separated from #79 we need to port ``` vtools init ceu --parent ../ --variants CEU --samples "RACE=1" --build hg19 ```
Perhaps it is worth noticing that HDF5 does not have error recovery mechanism and there are quite a few complaints if you google "corruption hdf5". Cautions have to be used...
A typical genotype entry looks like: `0/0:43,0:43:92:0,92,1267` The first part `0/0` is the actual genotype; the others are genotype annotations. In our current implementation (vat 2.0 hereafter) we import GT...
Rephrased from bug identified by @danielnachun: In our test, ``` import unittest from sos_notebook.test_utils import sos_kernel from ipykernel.tests.utils import execute, wait_for_idle, assemble_output ``` the last line does not work anymore,...
Raised today by @Bale4 who seems to have to manually adjust / rearrange columns for phenoIDFile when performing sQTL analysis. I think we should generate this file from our pipeline,...
@hsun3163 I'm raising this issue here, for there are problems recently reported due to obsolete or incomplete minimal working example commands as a result of changes made. I'll make a...
@hsun3163 this ticket keeps track of modules that I (re)reviewed : at this round I mostly make all the changes myself and try to finalize everything. Every time I finalize...