Kurt-Hetrick JHG_Clincal_Exome_Pipeline issues

Kurt-Hetrick / JHG_Clincal_Exome_Pipeline

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add git shorthash to submission notification

#55 Kurt-Hetrick opened 4 months ago
0
fix header for verifybam id per sample per chromosome report

#54 Kurt-Hetrick opened 4 months ago
0
add a bcftools split to pipeline mt vcf

#53 Kurt-Hetrick closed 4 months ago
8
create tool that can genotype any samples back from gvcfs

#52 Kurt-Hetrick opened 6 months ago
1
delete all jobs with specific project name

#51 Kurt-Hetrick opened 8 months ago
0
notify errors of non-critical failures

#50 Kurt-Hetrick opened 8 months ago
0
prepend emedgene folder name with family name

#49 Kurt-Hetrick closed 4 months ago
1
row number check for base distribution pct is not a number

#48 Kurt-Hetrick closed 4 months 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 2 years ago
1
remove sample count from file name of exomedepth controls rda files

#39 Kurt-Hetrick closed 2 years ago
4
make phase2 branch the active branch

#38 Kurt-Hetrick opened 2 years 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 3 years ago
1
clean-up annovar

#30 Kurt-Hetrick closed 2 years ago
2
increase vcf compression

#29 Kurt-Hetrick closed 3 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 3 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 3 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 3 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 3 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 2 years 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