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Kurt-Hetrick
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CIDR_WES
CIDR's production pipeline for WES and other targeted DNA sequencing projects.
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summarize differences between grch37 and grch38 pipelines
#87
Kurt-Hetrick
closed
5 years ago
1
fix target bed file name after formatting
#86
Kurt-Hetrick
closed
2 years ago
2
email summary doesn't send when jobs fail
#85
Kurt-Hetrick
closed
5 years ago
1
OXIDATION REPORT
#84
Kurt-Hetrick
closed
5 years ago
1
LOOK AT WALL CLOCK TIME SUMMARY CODE
#83
Kurt-Hetrick
closed
5 years ago
1
add samples that have multiple libraries to end of run summary
#82
Kurt-Hetrick
closed
2 years ago
2
fix job dependency for ends tasks in grch38 pipeline
#81
Kurt-Hetrick
closed
5 years ago
1
output qc reports paths to teams notifications
#80
Kurt-Hetrick
closed
5 years ago
2
update picard version used for liftover
#79
Kurt-Hetrick
closed
4 years ago
3
X.01-QC_REPORT_PREP: ANEUPLOIDY_CHECK columns shift
#78
bcraig110
closed
5 years ago
2
mark duplicate pixel distance
#77
Kurt-Hetrick
closed
5 years ago
2
stubs for read group headers
#76
Kurt-Hetrick
closed
5 years ago
1
calculate optical duplicate percentage
#75
Kurt-Hetrick
closed
5 years ago
2
update data dictionary for pcr dup metrics when multiple libraries are used
#74
Kurt-Hetrick
closed
5 years ago
1
mark duplicates not reporting total dup metrics when there are multiple libraries per samples
#73
Kurt-Hetrick
closed
5 years ago
6
combine vcf breakouts into one job
#72
Kurt-Hetrick
closed
2 years ago
2
remove MEAN_BAIT_COVERAGE
#71
Kurt-Hetrick
closed
5 years ago
1
test new version of picard for collecthsmetrics
#70
Kurt-Hetrick
closed
5 years ago
2
handle dual indexes when fastq is created from bam or cram file
#69
Kurt-Hetrick
closed
5 years ago
1
change R dependency to work on our RHEL7 servers
#68
Kurt-Hetrick
closed
5 years ago
1
make priority something that you can change
#67
Kurt-Hetrick
closed
5 years ago
1
have to add a new condition to find novaseq files that have gone through cram to fastq
#66
Kurt-Hetrick
closed
5 years ago
4
bwa find fastq breaks on symlinks
#65
Kurt-Hetrick
closed
5 years ago
1
fix regex for finding novaseq fastq files
#64
Kurt-Hetrick
closed
5 years ago
1
edit queue list
#63
Kurt-Hetrick
closed
5 years ago
1
add chrM to grch38 RefSeq file
#62
Kurt-Hetrick
closed
5 years ago
1
exclude MT from gvcf creation
#61
Kurt-Hetrick
closed
5 years ago
1
novaseq exome cap-off sequencing library names and mark duplicates
#60
Kurt-Hetrick
closed
5 years ago
1
create read me on test files
#59
Kurt-Hetrick
opened
5 years ago
0
handle when there are no fastq files for a sample
#58
Kurt-Hetrick
closed
5 years ago
1
update lab prep metrics tool
#57
Kurt-Hetrick
closed
4 years ago
3
handle blank rows in the samplesheet
#56
Kurt-Hetrick
closed
5 years ago
1
per chromosome verifybamid in one job instead of 1 job per chromosome
#55
Kurt-Hetrick
closed
5 years ago
2
email when finished submitting pipeline
#54
Kurt-Hetrick
closed
5 years ago
1
change picard version for liftover
#53
Kurt-Hetrick
closed
5 years ago
1
remove unplaced/unlocalized contigs from vcf after liftover
#52
Kurt-Hetrick
closed
5 years ago
1
collapse bed files
#51
Kurt-Hetrick
opened
5 years ago
1
make fix bed files a requirement for genotype scatter
#50
Kurt-Hetrick
closed
5 years ago
2
fix data dictionary
#49
Kurt-Hetrick
closed
5 years ago
3
handle gatk 4 jar file naming
#48
Kurt-Hetrick
closed
2 years ago
1
automatically make a copy of the final report with the sm tag
#47
Kurt-Hetrick
closed
2 years ago
1
bgzip/tabix refined ms vcf
#46
Kurt-Hetrick
closed
6 years ago
1
create readme referencing all of the software used
#45
Kurt-Hetrick
opened
6 years ago
0
upgrade sambamba 0.6.8
#44
Kurt-Hetrick
closed
4 years ago
1
need to look into double soft end clipping (bacteria) for gvcf creation
#43
Kurt-Hetrick
closed
2 years ago
1
make sure that everything is in percent from now on in qc report
#42
Kurt-Hetrick
closed
5 years ago
1
qc report: freemix header
#41
Kurt-Hetrick
closed
6 years ago
1
add substiuttion rates to qc report
#40
Kurt-Hetrick
closed
6 years ago
1
change bait vcf to union bed file for mendel
#39
Kurt-Hetrick
closed
5 years ago
2
disable autoindexing for select the vcfs for verifybamid steps
#38
Kurt-Hetrick
closed
6 years ago
1
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