Kurt-Hetrick CFTR_Full_Gene_Sequencing_Pipeline issues

Kurt-Hetrick / CFTR_Full_Gene_Sequencing_Pipeline

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update CFTR2

#65 Kurt-Hetrick opened 3 weeks ago
0
filter combined splicing with annovar file

#64 Kurt-Hetrick opened 3 weeks ago
0
row number check for base distribution pct is not a number

#63 Kurt-Hetrick opened 1 year ago
0
exit codes are not being set correctly in pre check validations

#62 Kurt-Hetrick opened 1 year ago
0
create readme on cmd line submissions

#61 Kurt-Hetrick closed 1 year ago
1
make hold id for md5 validation possible for multiple projects

#60 Kurt-Hetrick closed 1 year ago
2
md5 validation check only sends mail when verbose

#59 Kurt-Hetrick closed 1 year ago
1
check that local git-lfs repo does not have committed changes not pushed to remote

#58 Kurt-Hetrick closed 2 years ago
1
capture git lfs commit hash

#57 Kurt-Hetrick closed 1 year ago
2
build option to ignore that git-lfs resource directory has new files

#56 Kurt-Hetrick closed 1 year ago
1
generate md5 for for git-lfs. compare to static file.

#55 Kurt-Hetrick closed 1 year ago
3
check that git-lfs has no untracked or uncommitted changes

#54 Kurt-Hetrick closed 2 years ago
1
create a version release

#53 Kurt-Hetrick closed 2 years ago
1
remove version and timestamp in CF_CFTR.NGS1.v1.140604.bed filename

#52 Kurt-Hetrick closed 2 years ago
1
remove version and timestep in CF_CFTR.NGS1.v1.140604.bed filename

#51 Kurt-Hetrick closed 2 years ago
1
remove e flag in set pipefail wherever it is

#50 Kurt-Hetrick opened 2 years ago
0
replace combinevariants with a new tool

#49 Kurt-Hetrick opened 2 years ago
1
sv calls outside of cftr transcript in cftr2 report

#48 Kurt-Hetrick opened 3 years ago
0
pipeline auxiliary files should be tracked via gitlfs

#47 Kurt-Hetrick closed 2 years ago
2
undeclared variable used in samtools qc report stub generation

#46 Kurt-Hetrick closed 3 years ago
1
cftr2 report small variants is tab delimited when there are no variants

#45 Kurt-Hetrick closed 3 years ago
1
cleanup annovar output

#44 Kurt-Hetrick closed 3 years ago
1
bwa does not exit non-zero on failure

#43 Kurt-Hetrick opened 3 years ago
0
run verifybamid twice

#42 Kurt-Hetrick closed 3 years ago
1
change end project tasks

#41 Kurt-Hetrick closed 3 years ago
2
switch end task to -pe slots instead of exclusive=true

#40 Kurt-Hetrick closed 3 years ago
1
need to rebuild r container used to merge annovar output with splicing algorithms

#39 Kurt-Hetrick closed 3 years ago
1
manta config file/directory needs to be deleted if being reran

#38 Kurt-Hetrick opened 3 years ago
0
need mechanism to update annotated cftr2 reports/vcf files

#37 Kurt-Hetrick opened 3 years ago
1
bait bias fails when there is only one interval

#36 Kurt-Hetrick opened 3 years ago
0
CFTR2 report pass/fail for small variants

#35 Kurt-Hetrick closed 3 years ago
1
force overwriting index when using tabix to index compressed vcf

#34 Kurt-Hetrick closed 3 years ago
1
add manta filter to cftr2 output

#33 Kurt-Hetrick closed 3 years ago
1
double check poly TG T tract location

#32 Kurt-Hetrick closed 3 years ago
1
fix cftr2 lists

#31 Kurt-Hetrick closed 3 years ago
1
liftover cftr2 variants

#30 Kurt-Hetrick closed 3 years ago
1
manta vcf to bedpe?

#29 Kurt-Hetrick closed 3 years ago
3
add thread variable

#28 Kurt-Hetrick closed 3 years ago
1
add sm tag to depth of coverage reports

#27 Kurt-Hetrick closed 3 years ago
1
write a lightweight utility to merge all batch qc reports together?

#26 Kurt-Hetrick closed 3 years ago
2
md5 on remaining files

#25 Kurt-Hetrick closed 3 years ago
1
do batch qc report

#24 Kurt-Hetrick closed 3 years ago
1
look into summarizing/normalzing allele balance/depth info for X an Y barcode snps/regions.

#23 Kurt-Hetrick opened 3 years ago
0
structural variant annotation

#22 Kurt-Hetrick closed 3 years ago
1
decompose/normalize vcf file before running annovar

#21 Kurt-Hetrick closed 3 years ago
1
fisher strand bias cut-off

#20 Kurt-Hetrick closed 3 years ago
1
updating dbsnp annotation in vcf?

#19 Kurt-Hetrick closed 3 years ago
2
implement qc report

#18 Kurt-Hetrick closed 3 years ago
1
bait,target,titv bed files

#17 Kurt-Hetrick closed 3 years ago
2
do summary coverage report for cftr exon intervals.

#16 Kurt-Hetrick closed 3 years ago
1