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Name in trackqc bam #105

Merged
merged 48 commits into from Jun 11, 2012
Merged

Name in trackqc bam #105

merged 48 commits into from Jun 11, 2012

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andrewjpage
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sb10 and others added 30 commits May 14, 2012 17:24
@sb10
script to dump asana to a tab-separated file
24c2ae0
@sb10
added option to output a gz file with todays date to the supplied dir
6b40726
@jm23
moving compression step elsewhere
f529e5a
@pd3
Wrapper for mouse QC to artifically reduce duplicate rate by ignoring…
06dce8b 
… known high-coverage regions
@pd3
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase in…
aafc935 
…to develop
@jm23
the tinkerer returns without a date
73401b0
@pd3
Prevent uninitialized variable warning when DP not present
18e9a3a
@pd3
Significant speedup of event_type for very large REFs and ALTs
4acc1d3
@pd3
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase in…
987f701 
…to develop
@pd3
Added -f, -F options. Count and plot indels per cycle for each mate p…
5f4eb9e 
…air separately.
@pd3
Added the possibility to add header lines and another example of a us…
16e1c2d 
…er-defined filter.
@jm23
script for sql dump compression
161938c
@jm23
permissions altered
54af15c
@pd3
Handle haploid GLs
04871cd
@pd3
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase in…
7fd9930 
…to develop
@pd3
Skip HWE calculation at multiallelic sites
b18645e
@pd3
Now annotates also the QUAL column
ab4a580
@jm23
new script for weekly new lanes report
0534cf1
@jm23
removing zero counts
55385fd
@pd3
Include the total number of indels in the statistics
7050432
@pd3
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase in…
fa2c8d9 
…to develop
@mcshane
add option to force adding readgroup
c82dbb8
@pd3
GapWin take advantage of AC when AF not present; use real del length …
831e0fb 
…and 1bp for inserts
@pd3
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase in…
d02246a 
…to develop
@sb10
fixed bug where it could not parse tasks with complex notes
12a5548
@sb10
added ability to output user-centric html for use in team meetings on…
c1badb9 
… mobile phones; changed command line options
@sb10
now that it does more than output tsv, changing name
48f4261
@sb10
uncommented print of html header
84e2046
@pd3
VQSR filtering
dc52d11
@pd3
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase in…
39fc3a4 
…to develop
pd3 and others added 18 commits May 30, 2012 13:20
@pd3
Lightweight script for calculating Ts/Tv ratio
7fe6746
@mcshane
let -a option work when -c option not given
7bc9851
@pd3
Run VQSR separately for SNPs and indels
4e1693d
@pd3
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase in…
32fe2ec 
…to develop
@kw10
Modified Breakdancer bam2cfg.pl to include more statistics for calcul…
930aa94 
…ation of SD cutoff value; density.R file is required
@cj5-sanger
changed mapped col from mapstats->raw_bases() to mapstats->bases_mapp…
51211e9 
…ed()
@cj5-sanger
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase in…
7ef0ac8 
…to develop
@cj5-sanger
minor formatting changes
7c0ba01
@sb10
added some help text to clarify meaning of last 3 columns
67f4aa7
@sb10
slightly better name for last column
d0d1cd4
@pd3
Allow -a just by itself
be4d554
@jm23
adding find species by taxon id for new update pipeline
4d3aa95
@pd3
Report number of multiallelic SNP sites
e852300
@pd3
Do VQSR training on concatenated VCF, not per chromosome
4c42a7d
@pd3
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase in…
a059d9f 
…to develop
@pd3
Another number into the stats: the number of SNPs
ee9e1d0
@andrewjpage
Merge branch 'develop' of http://github.com/VertebrateResequencing/vr…
1dc4381 
…-codebase into pipeline
@andrewjpage
declare bam name
13ac90a
andrewjpage added a commit that referenced this pull request Jun 11, 2012
@andrewjpage
Merge pull request #105 from andrewjpage/name_in_trackqc_bam
6ce27f0 
Name in trackqc bam
@andrewjpage andrewjpage merged commit 6ce27f0 into sanger-pathogens:pipeline Jun 11, 2012
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7 participants
@andrewjpage @sb10 @jm23 @pd3 @mcshane @kw10 @cj5-sanger