vatlab varianttools issues

vatlab / varianttools

software tool for the manipulation, annotation, selection, and analysis of variants in the context of next-gen sequencing analysis

https://vatlab.github.io/vat-docs/

GNU General Public License v3.0

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issues

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Weird imported VAF float field from VCF

#160 guillaumecharbonnier closed 1 year ago
3
patch for row.c

#159 jenningsje closed 2 years ago
0
fixed bugs in row.c

#158 jenningsje closed 2 years ago
0
editing line 220

#157 jenningsje closed 2 years ago
1
fixed bugs in row.c

#156 jenningsje opened 2 years ago
1
fixed bugs in row.c

#155 jenningsje closed 2 years ago
0
Cannot be built with Python 3.9

#154 rekado closed 1 year ago
4
SPECFILE not available in Variant Simulation Tools

#153 enigmargs closed 3 years ago
3
Hg38 support

#152 akshayzawar closed 3 years ago
3
All association tests have failed (Association tests on 324063 groups have completed. 324063 failed)

#151 marionamujal opened 4 years ago
2
Association analysis running but remains at 0% for hours

#150 marionamujal opened 4 years ago
4
WARNING: hg19: Failed to get reference sequence: unrecognized chromosome id: 65535

#149 marionamujal closed 4 years ago
9
KING 2.2.4

#148 Yomiran opened 4 years ago
1
KING pipeline does not work

#147 BoPeng opened 4 years ago
5
Failed to import insertion

#146 BoPeng closed 4 years ago
0
vtools import --store sqlite

#145 BoPeng closed 4 years ago
0
Python 3.8 use spawn as default method to create subprocesses.

#144 BoPeng opened 4 years ago
3
Switch Variant Tools from MD Anderson to a public hosting location (AWS?)

#143 BoPeng opened 4 years ago
0
Association test with covariate depending on the gene-set

#142 fabiennejh opened 4 years ago
4
DP_geno is not parsing genotype fields

#141 enigmargs closed 4 years ago
27
SKAT test not displayed under `vtools show test`

#140 BoPeng closed 4 years ago
1
Fisher exact test pvalue and multiple testing

#139 freedomq8 opened 4 years ago
9
SKAT errors

#138 BoPeng opened 4 years ago
6
vtools access to annotation database

#137 BoPeng opened 4 years ago
0
Error when output variants of samples with genotype value as filter criteria

#136 mullinyu opened 4 years ago
1
ERROR: Cannot find reference genome for build hg19: Unknown runtime error happened.

#135 FianaNG closed 4 years ago
28
Documentation not viewable on cell phones

#134 BoPeng opened 5 years ago
0
"object name is not a valid python identifier" during vtools associate.

#133 BoPeng closed 5 years ago
1
git hook for pyflakes and yapf formatter

#132 BoPeng closed 5 years ago
5
Install error on latest version

#131 jma7 closed 5 years ago
9
KING version 2.1.4 and 2.2.4 different results

#130 gaow closed 5 years ago
1
HDF5 group regenerated warning

#129 gaow closed 5 years ago
0
vtools export bug

#128 gaow closed 5 years ago
19
index out of range from 'vtools associate'

#127 BoPeng closed 5 years ago
1
Slowness of `vtools show genotypes`

#126 BoPeng closed 4 years ago
1
Undefined HMatrix type

#125 BoPeng closed 5 years ago
1
Add a edit in github button to documentation

#124 BoPeng opened 5 years ago
0
Suppress NumExpr message

#123 BoPeng closed 5 years ago
1
Stop embedding boost, zeromq, and gsl

#122 BoPeng closed 5 years ago
2
Failed to import module (No module named '_cgatools')

#121 smcgrat closed 5 years ago
14
`vtools select` doesnt work when selecting variants for given samples

#120 gaow closed 5 years ago
27
gene set based burden test

#119 qserenali opened 5 years ago
3
Problems with samples() function

#118 BoPeng closed 4 years ago
10
database is locked

#117 qserenali opened 5 years ago
1
Compatibility with gcc 7.2

#116 BoPeng closed 5 years ago
7
Add scipy as dependency

#115 BoPeng closed 5 years ago
1
limit analysis based on selected region (bed file)

#114 freedomq8 opened 5 years ago
1
importing variants and no space left on device /tmp

#113 freedomq8 closed 5 years ago
1
Faster access to HDF5 using vaex

#112 BoPeng opened 5 years ago
1
zarr storage library

#111 BoPeng closed 4 years ago
0