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Multiple enhancements and bugfixes #164

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Multiple enhancements and bugfixes #164

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@jscaber jscaber commented Dec 17, 2024

Enhancements

  • Rewritten exome pipeline bringing it in line with GATK4 changes
  • Exome: replaced ancestry (inclompletely implemented) by somelier tool
  • rMATS output filtering

Bugfixes

  • splicing pipeline
  • cgatflow compatibility with python 3.12
  • compatibility with newer versions of sqlalchemy up to 8 (but not compatible with 9 - change in authentication method)
  • some removal of rpy2
  • removed strand specificity from bamstatc which has been removed from cgat apps

Miscellaneous

  • removed mappinqc.py which was a duplicate
  • removed unused scriptsdir
  • diff expression pipeline - handling of unexpected input

jscaber added 30 commits February 10, 2022 21:52
@jscaber
remove scriptsdir
86fb87e
@jscaber
remove scriptsdir
b90a82f
@jscaber
substatial changes to exome pipeline - bringing it in line with pipel…
482a294 
…ine bamstats and changes in gatk
@jscaber
remove mappingqc from pipeline_mapping.py
40fb76e
@jscaber
remove mappingqc from pipeline_windows.py
bfbb604
@jscaber
remove mappingqc from pipeline peakcalling
f2e5451
@jscaber
remove mappingqc from rnaseqqc pipelin
37f5213
@jscaber
remove mappingqc from exome cancer pipeline
cc83e76
@jscaber
remove mappingqc.py - obsolete and superseded by bamstats.py
5f63ab3
@jscaber
fixing errors
61427c4
@jscaber
troubleshooting
d1792d1
@jscaber
troubleshooting
2c3aabf
@jscaber
Removed realignment step as per GATK4
a433956
@jscaber
updated BSQR procedure to gatk4 syntax
d377b33
@jscaber
Merge branch 'JS-current' into JS-exome
00ede33
@jscaber
Gatk4 update: GVCF and GVCF database
0b960e6
@jscaber
Merge branch 'master' into JS-exome
5b8473d
@jscaber
gatk4: GenotypeGVCF now from database
52b67d0
@jscaber
added options for rMATS output filtering (results table) - FDR, PSI a…
6be599f 
…nd coverage
@jscaber
options for pipeline splicing - yml file update
aaaf87f
@jscaber
snpeff updated
cb62f8c
@jscaber
bug corrections pipeline splicing
75b3ef4
@jscaber
further bugfixes splicing pipeline
e406b90
@jscaber
major changes exome pipeline
37ed54b 
- rearrangement of pipeline
- completed gatk best practices
- started variant annotation updates
@jscaber
replace hapmap by somelier
0834b14
@jscaber
remove xy prediction, which is provided by other tools and previous e…
a3bf625 
…xecution not ideal
@jscaber
Exome Pipeline Development
2e56974 
- fixes for annotations
- removal of ancestry functions, better covered by somalier
- removal of remaining sex estimation functions
@jscaber
bugfixes exome pipeline:snpsift and revomal exomeancestry.py
4143583
@jscaber
snpsift bugfixes
5f081d9
@jscaber
Add SpliceAI
a589335
jscaber added 15 commits May 16, 2022 10:27
@jscaber
further exome pipeline - removed pedigree analysis
39e993e 
- now also runs VEP on vcf
- annotation pipeline completed
@jscaber
remove pedigree pipeline
0769f35
@jscaber
functions to establish gene 'Panel' BED from list
d6685f3 
further cleanup
further rearrangement
VEP output now txt
@jscaber
various improvements to diff expression pipeline - able to handle une…
3231f31 
…xpected data
@jscaber
Extensive changes to exome pipeline, bamstats and exploratory analysis
af5661a
@jscaber
chages to exome.py
a0524b9
@jscaber
further development
9342ccb
@jscaber
addition of setup instruction for R tools
a78a149
@jscaber
draft long read pipeline
5ed4039
@jscaber
Cchanges to cgatflow.py, compatibility with python 3.12
fccb2f1
@jscaber
remove rpy2
e6275ba
@jscaber
add R scripts to new directory
32cac1e
@jscaber
add further R scripts, moved
00dffe9
@jscaber
Changes to Make GTFsubset compatible with sqlachemy changes
563dd06
@jscaber
remove strand specificity which has been removed from cgat apps
d960eed
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@jscaber