FINNGEN META_ANALYSIS issues

FINNGEN / META_ANALYSIS

Tools for doing x way meta-analysis

MIT License

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issues

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Split qc histograms by AF

#65 juhaa opened 3 months ago
0
Munge pipeline plots AF comparison to gnomad after filtering

#64 juhaa opened 3 months ago
0
Bugfix: Added dummy SNP column for manhattan function in qqman

#63 samuelejones closed 5 months ago
0
Citation

#62 karpat90 opened 9 months ago
1
QC upgrades

#61 juhaa closed 10 months ago
0
allow final newline, allow non-tab delim, don't assume chr and pos co…

#60 juhis closed 1 year ago
1
liftover fails when reaching last line of sumstats

#59 Fedja closed 1 year ago
0
Optimize QC

#58 juhaa closed 1 year ago
0
Plotting scripts read the input only partially

#57 juhaa closed 1 year ago
0
Remove unnecessary defaultdicts

#56 juhaa opened 2 years ago
0
Disable sorting in liftover call

#55 juhaa opened 2 years ago
0
New QC stuff

#54 juhaa closed 1 year ago
0
Check for compulsory columns and error out

#53 Fedja opened 2 years ago
0
Replace dont_allow_space with sep

#52 juhaa closed 2 years ago
0
add to readme how to run production analyses

#51 Fedja opened 2 years ago
0
Does not align to all references in the same position

#50 Fedja closed 2 years ago
2
Handling duplicates

#49 juhaa closed 2 years ago
0
Transformed p-values can cause issues in munging

#48 juhaa opened 2 years ago
0
WDL 1.0

#47 juhaa closed 2 years ago
0
Add filter for af difference & don't flip indels by default

#46 juhaa closed 2 years ago
0
Duplicate SNPs are not handled properly

#45 juhaa closed 2 years ago
2
Add mlogp column to results

#44 juhaa closed 2 years ago
0
Use -log10 space for p-values

#43 juhaa closed 2 years ago
1
Leave-one-out analysis has missing fields

#42 juhaa closed 3 years ago
0
Fix harmonization messing up column order

#41 juhaa closed 3 years ago
0
Picard liftover

#40 juhaa closed 3 years ago
0
Harmonization messes up column ordering

#39 juhaa closed 3 years ago
3
Replace fold change with absolute difference

#38 juhaa closed 3 years ago
0
Add liftover wdl

#37 juhaa closed 3 years ago
1
use absolute AF difference to pick closest one...

#36 Fedja closed 3 years ago
0
Minor WDL updates

#35 juhaa closed 3 years ago
0
biobanks meta GWAS data sharing

#34 montenegrina opened 3 years ago
0
Workflows for preprocessing and post-meta stuff

#33 juhaa closed 3 years ago
0
Input file row values not read correctly if missing values

#32 juhaa closed 2 years ago
4
Create pre-processing pipeline for qc and harmonization of studies for meta-analysis

#31 Fedja closed 2 years ago
6
Duplicate variants which are deemed equal not always properly aligned

#30 juhaa closed 3 years ago
1
Check for another variant in same position

#29 juhaa closed 3 years ago
1
Add wdl with qc plots

#28 juhaa closed 3 years ago
1
Multiple variants in same position not correctly matched when analyzing single chromosome

#27 juhaa closed 3 years ago
1
Fix chrX incorrect conversions when --chrom set

#26 juhaa closed 3 years ago
2
Incorrect conversion/comparison of chromosome names when --chrom used

#25 juhaa closed 3 years ago
0
Fix for when a list element is None from do_meta

#24 juhaa closed 3 years ago
6
Error when right variant has NA values

#23 juhaa closed 3 years ago
0
Added Jenkins support and unit tests

#22 majorseitan opened 4 years ago
0
WDL feature: Adding tsv headers to lift.files

#21 sinarueeger closed 2 years ago
0
Revert "Covid meta jk"

#20 juhis closed 4 years ago
0
Covid meta jk

#19 juhis closed 4 years ago
0
add heterogeneity tests

#18 weizhouUMICH closed 4 years ago
0
x/y/mt without chr prefix

#17 juhis closed 4 years ago
0
We also will want to include pre-meta QC steps, including detecting potential sample overlapping

#16 weizhouUMICH opened 4 years ago
0