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single sample processing for pindel cohort #96

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single sample processing for pindel cohort #96

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keiranmraine and others added 30 commits January 13, 2020 10:12
@keiranmraine
Apply fix provided Bt Kai Ye/Xiaofei Yang to recover missed complex e…
86e99c8 
…ven (known to be real)
@keiranmraine
Apply fix provided Bt Kai Ye/Xiaofei Yang to recover missed complex e…
d5726b4 
…ven (known to be real)
@keiranmraine
deletions working, cleaned up install process
a2a1bcd
@keiranmraine
Simple del/ins "working", but looks like switch in parsing format is …
3251131 
…needed
@keiranmraine
Initial pass at cohort pindel processing, no visualisation outputs (B…
51296ce 
…AM/CRAM) just VCF
@keiranmraine
Merge pull request #89 from cancerit/feature/insertLargerThanDel
ca37b83 
Apply fix provided Bt Kai Ye/Xiaofei Yang to recover missed complex e…
@keiranmraine
Functional cohort sample code with blat and BAM outputs
49ecb5f
@keiranmraine
Script for assessing impact of different lengths of target seq
79a822f
@keiranmraine
Correct missing param default
e831ae6
@keiranmraine
minor fixes
e8f7868
@keiranmraine
Final version of plots
50eaaee
@keiranmraine
Fix bug in read selection, performance implications but best I can th…
7302b1d 
…ink of
@keiranmraine
cleanup
9fa478b
@keiranmraine
lazy stuff
477a0e6
@keiranmraine
convert to have ability to work on multisample VCF
8f9d163
@keiranmraine
working towards vaf fill in
e166a67
@keiranmraine
fix conflict during merge
673609c
@keiranmraine
Working fill-in code
cee0c94
@keiranmraine
Finalise last of cohort processing scripts
67b6445
@keiranmraine
Update tests for changes to how data is passed
9ae6799
@keiranmraine
Minor updates to deploy
c263413
@keiranmraine
Cleanup following bug hunt
0c385bb
@keiranmraine
Final few issues with change to compressed files handled.
11d1ed0
@keiranmraine
reduce change of exceptionally high number of files in a single direc…
c3edc49 
…tory
@keiranmraine
Fix up cohort tools that share VcfBlatAugment object for changes to c…
e61a3a9 
…onstructor and files
@keiranmraine
typo
a15da93
@keiranmraine
Cleanup so restarts work if failure occured during samtools sort
538b077
@keiranmraine
some lagging differences
01e4f38
@keiranmraine
docker cleanup
ea0b2c4
@keiranmraine
add in new filter form Stan
08135e5
keiranmraine
keiranmraine commented Sep 8, 2021
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Self review to sanity check. Tests in place and output of code deemed ready for production use has been reviewed by scientific staff.

@keiranmraine keiranmraine marked this pull request as ready for review September 8, 2021 15:10
keiranmraine and others added 21 commits October 6, 2021 14:03
@keiranmraine
Iterative improvement to calls
31b8b7e
@keiranmraine
Some simple util scripts for generating data grids
12c8600
@keiranmraine
Faster blats due to reduced read parsing when multiple hits at same l…
ab98c3b 
…oci (common)
@keiranmraine
missing licenses
c1afb9e
@keiranmraine
current state
4f6b59e
@keiranmraine
Improves large del processing
bd547b8
@keiranmraine
Addition of simple repeat filters
1a10d7b
@keiranmraine
bring in recent changes from dev
eca430e
@keiranmraine
some docs
83af748
@rulixxx
Update Implement.pm
bf3e985 
added pipefail option for pindel commands
@rulixxx
Update pindelCohortVafSliceFill.pl
03a97dd 
Fixed simple repeat input parameter
@rulixxx
Update pindelCohortVafSliceFill.pl
cb472f9 
corrected spelling error
@rulixxx
metanorm filtering rules
8f53e43
@rulixxx
Create metanormRules.lst
9113d8a
@rulixxx
Update Pindel.pm
ac057fb 
Added version for cohort code
@rulixxx
Update Implement.pm
cb8479a 
Added version number for cpindel
@rulixxx
Update Implement.pm
b1be25f
@rulixxx
Update CHANGES.md
4eab4bd 
Removed all pindel stuff, made realease 1.0.0 of cpindel
@rulixxx
Update Implement.pm
93839f5 
Added a test of the sam.gz file created by blat
upped version
66dd39d
reformatted blat command
011bd27
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@keiranmraine @rulixxx