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populationgenomics
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saige-tenk10k
Hail batch pipeline to run SAIGE on CPG's GCP
MIT License
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RV pipeline debug
#171
annacuomo
closed
1 day ago
0
Test config
#170
annacuomo
closed
2 days ago
1
dumb
#169
annacuomo
closed
2 days ago
1
small tweaks
#168
annacuomo
closed
3 days ago
1
Conditional analysis newfile with in-job looping
#167
MattWellie
opened
3 days ago
1
starting conditional analysis as a new file
#166
annacuomo
opened
5 days ago
0
rebase conditional analysis branch
#165
annacuomo
closed
5 days ago
0
Update demux script
#164
annacuomo
closed
6 days ago
1
Maf not alt freq
#163
annacuomo
closed
6 days ago
0
always subset by locus first when doing locus and sample
#162
Alexander-Stuckey
closed
6 days ago
0
Readme updates
#161
annacuomo
opened
6 days ago
0
tweak tweak
#160
MattWellie
closed
6 days ago
3
start adding to conditional analysis
#159
annacuomo
closed
5 days ago
1
start adding to writeout file writing
#158
annacuomo
closed
6 days ago
5
add common or rare flag
#157
annacuomo
closed
1 week ago
0
Rename filepath from set to rare
#156
annacuomo
closed
1 week ago
0
update the docstring with example usage
#155
Alexander-Stuckey
closed
1 week ago
0
output data to analysis
#154
Alexander-Stuckey
closed
1 week ago
0
maybe this?
#153
MattWellie
closed
1 week ago
0
add single variant results rare test
#152
annacuomo
closed
1 week ago
2
New sex files
#151
annacuomo
closed
1 week ago
0
add cis gene job mem also
#150
annacuomo
closed
1 week ago
0
More efficiencies
#149
MattWellie
closed
1 week ago
7
Write to a valid local path
#148
MattWellie
closed
1 week ago
0
Peak efficiency
#147
MattWellie
closed
1 week ago
0
first attempt at parallelising make group file
#146
annacuomo
closed
1 week ago
0
Address Katie's get_anndata.py issue (#73)
#145
annacuomo
closed
1 week ago
0
Address Katie's get_genotype_vcf.py issue (#71)
#144
annacuomo
closed
1 week ago
6
Update instructions at top of scripts
#143
annacuomo
closed
1 week ago
0
Better path name
#142
annacuomo
closed
2 weeks ago
0
update output paths for rv also
#141
annacuomo
closed
2 weeks ago
0
Update readme rv
#140
annacuomo
closed
2 weeks ago
0
Groupfile cleanup
#139
annacuomo
closed
2 weeks ago
0
RV pipeline clean up
#138
annacuomo
closed
2 weeks ago
0
feat: pas-446 create a vds subsetting script
#137
Alexander-Stuckey
closed
1 week ago
2
results are in analysis bucket
#136
annacuomo
closed
2 weeks ago
0
adding weight specs back in
#135
annacuomo
closed
2 weeks ago
1
only take var pos for distances
#134
annacuomo
closed
3 weeks ago
2
more variants no weight name
#133
annacuomo
closed
3 weeks ago
1
test weight name
#132
annacuomo
closed
3 weeks ago
1
add test weights
#131
annacuomo
closed
3 weeks ago
1
test single variant, test anno
#130
annacuomo
closed
3 weeks ago
1
change ids to match with :
#129
annacuomo
closed
3 weeks ago
0
Update variant format groupfile
#128
annacuomo
closed
3 weeks ago
0
space separated instead of tab
#127
annacuomo
closed
3 weeks ago
0
weights as option in group file
#126
annacuomo
closed
3 weeks ago
1
make group file without weights
#125
annacuomo
closed
3 weeks ago
1
Modify SAIGE-QTL RV flags / args for debugging
#124
annacuomo
closed
3 weeks ago
1
group file should be tab separated
#123
annacuomo
closed
1 month ago
1
remove $ sign
#122
annacuomo
closed
1 month ago
0
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