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aryarm
/
as_analysis
A complete Snakemake pipeline for detecting allele specific expression in RNA-seq
MIT License
10
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extract gq into one file
#29
aryarm
closed
6 years ago
1
switch to tsv's
#28
aryarm
closed
6 years ago
0
gzip all of the things
#27
aryarm
closed
6 years ago
1
investigate heterozygotes in counts data
#26
aryarm
closed
6 years ago
0
add vqsr filtering for indels?
#25
aryarm
closed
6 years ago
1
set min snakemake version
#24
aryarm
closed
6 years ago
0
clean up repo
#23
aryarm
closed
6 years ago
1
rewrite config files to take advantage of yaml
#22
aryarm
closed
4 years ago
3
incorporate hard filtering into variant calling pipeline
#21
aryarm
closed
6 years ago
0
use wildcards to get_as_counts dna/rna
#20
aryarm
closed
6 years ago
0
samtools mutli threading
#19
aryarm
closed
6 years ago
0
provide flexibility for specifying samples
#18
aryarm
closed
4 years ago
5
include index files in all rules
#17
aryarm
closed
6 years ago
0
refine python code in Snakefiles
#16
aryarm
closed
6 years ago
0
redevelop find_imbalance.r for multiple samples
#15
aryarm
closed
6 years ago
1
running entire pipeline all at once
#14
aryarm
closed
6 years ago
1
shadow rules
#13
aryarm
closed
6 years ago
4
split Snakefile
#12
aryarm
closed
6 years ago
1
specifying specific samples
#11
aryarm
closed
6 years ago
0
incorporate R script into Snakefile
#10
aryarm
closed
6 years ago
1
incorporate WASP pipeline back into Snakefile
#9
aryarm
closed
6 years ago
0
test final.bash equivalent of snakemake pipeline
#8
aryarm
closed
6 years ago
0
create config option for base score and variant score recalibration
#7
aryarm
closed
6 years ago
1
named pipes
#6
aryarm
closed
6 years ago
1
use snakemake validation
#5
aryarm
opened
6 years ago
1
reference genome index files
#4
aryarm
opened
6 years ago
4
multi-threading for gatk
#3
aryarm
closed
6 years ago
1
conda envs
#2
aryarm
closed
6 years ago
1
wasp mode of STAR
#1
aryarm
closed
6 years ago
3
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