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Kurt-Hetrick
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JHG_Clincal_Exome_Pipeline
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add a bcftools split to pipeline mt vcf
#53
Kurt-Hetrick
closed
2 days ago
8
create tool that can genotype any samples back from gvcfs
#52
Kurt-Hetrick
opened
1 month ago
1
delete all jobs with specific project name
#51
Kurt-Hetrick
opened
3 months ago
0
notify errors of non-critical failures
#50
Kurt-Hetrick
opened
3 months ago
0
prepend emedgene folder name with family name
#49
Kurt-Hetrick
closed
2 days ago
1
row number check for base distribution pct is not a number
#48
Kurt-Hetrick
closed
2 days ago
1
exit codes are not being set correctly in pre check validations
#47
Kurt-Hetrick
opened
1 year ago
0
create readme on cmd line submissions
#46
Kurt-Hetrick
closed
1 year ago
1
check that local git-lfs repo does not have committed changes not pushed to remote
#45
Kurt-Hetrick
closed
1 year ago
1
capture git lfs commit hash
#44
Kurt-Hetrick
closed
1 year ago
2
build option to ignore that git-lfs resource directory has new files
#43
Kurt-Hetrick
closed
1 year ago
1
generate md5 for for git-lfs. compare to static file.
#42
Kurt-Hetrick
closed
1 year ago
4
check that git-lfs has no untracked or uncommitted changes
#41
Kurt-Hetrick
closed
1 year ago
1
create phase2-dev branch
#40
Kurt-Hetrick
closed
1 year ago
1
remove sample count from file name of exomedepth controls rda files
#39
Kurt-Hetrick
closed
1 year ago
4
make phase2 branch the active branch
#38
Kurt-Hetrick
opened
1 year ago
2
possibly make submission notification more verbose
#37
Kurt-Hetrick
closed
2 years ago
1
host operating system too old
#36
Kurt-Hetrick
opened
2 years ago
0
create protocol for regenerating reference panels for exomeDepth
#35
Kurt-Hetrick
opened
2 years ago
1
merge mt qc metrics into overall qc report.
#34
Kurt-Hetrick
closed
2 years ago
1
collect files used in emedgene into one folder
#33
Kurt-Hetrick
closed
2 years ago
1
send teams notification if snp vqsr fails once
#32
Kurt-Hetrick
closed
2 years ago
3
updating picard tools version for core exome pipeline
#31
Kurt-Hetrick
opened
2 years ago
1
clean-up annovar
#30
Kurt-Hetrick
closed
2 years ago
2
increase vcf compression
#29
Kurt-Hetrick
closed
2 years ago
1
base distribution report average per cycle, base substitution rate
#28
Kurt-Hetrick
closed
3 years ago
1
percentages in qc report are now reported as such
#27
Kurt-Hetrick
closed
3 years ago
2
MT bam out
#26
Kurt-Hetrick
closed
2 years ago
1
bug in *.VQSR.PASS.SNV.KinshipIBS.txt output in pca/relatedness script
#25
Kurt-Hetrick
closed
3 years ago
1
decompose vcf before annovar
#24
Kurt-Hetrick
closed
3 years ago
1
is bedtools or tabix faster when subsetting for handling overlapping deletions
#23
Kurt-Hetrick
closed
3 years ago
1
use sort -V for sorting by karyotype order
#22
Kurt-Hetrick
closed
3 years ago
1
consider creating the derived variables in the submitter as opposed to the execution script
#21
Kurt-Hetrick
closed
3 years ago
1
update exomeDepth container
#20
Kurt-Hetrick
closed
2 years ago
1
consider upgrading annotSV
#19
Kurt-Hetrick
closed
2 years ago
1
refactor the living daylights of all the things
#18
Kurt-Hetrick
closed
2 years ago
1
create ref panel sets for cnv workflow
#17
Kurt-Hetrick
closed
2 years ago
2
create bed files for cnv workflow
#16
Kurt-Hetrick
closed
3 years ago
1
dynamically generate total possible length of cnv calls
#15
Kurt-Hetrick
closed
3 years ago
1
remove mark duplicates dependency for fix bed files
#14
Kurt-Hetrick
closed
3 years ago
1
why is the order of CREATE_FAMILY_ARRAY and build hold flipped
#13
Kurt-Hetrick
closed
2 years ago
1
create fixed bed files per family
#12
Kurt-Hetrick
closed
3 years ago
1
multiple projects in sample sheet
#11
Kurt-Hetrick
closed
2 years ago
1
pca and relatedness
#10
Kurt-Hetrick
closed
3 years ago
1
haplotype caller bam gather should not be a blocking task
#9
Kurt-Hetrick
closed
1 year ago
1
file names too long for some reports
#8
Kurt-Hetrick
closed
2 years ago
1
create a slimmed down coverage report
#7
Kurt-Hetrick
closed
3 years ago
2
implement mt pipeline
#6
Kurt-Hetrick
closed
3 years ago
1
implement cnv pipeline
#5
Kurt-Hetrick
closed
3 years ago
2
implement ROH
#4
Kurt-Hetrick
closed
3 years ago
1
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