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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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write a generalized demuxing pipeline for novaseqx
#135
Kurt-Hetrick
opened
5 months ago
0
switch to doing concordance on grch38 arrays
#134
Kurt-Hetrick
closed
4 months ago
2
for novaseq runs. look for directory and file naming schemes used by bcl2fastq old school edition for fastq files.
#133
Kurt-Hetrick
opened
8 months ago
0
revamp fastq file lookup for the umpteenth time
#132
Kurt-Hetrick
opened
10 months ago
0
minor issue
#131
Kurt-Hetrick
opened
10 months ago
0
make duplicate metrics more robust when multiple libraries are used and one of them is trash
#130
Kurt-Hetrick
opened
1 year ago
0
validate bed files have proper contig names near beginning of submitters
#129
Kurt-Hetrick
opened
1 year ago
0
add 100x to coverage reports
#128
Kurt-Hetrick
closed
1 year ago
1
row number check for base distribution pct is not a number
#127
Kurt-Hetrick
closed
1 year ago
1
revamp fastq file lookup
#126
Kurt-Hetrick
closed
1 year ago
1
look for miseq files that have been demuxed with illumina bcl2fastq
#125
Kurt-Hetrick
closed
1 year ago
1
make sqe queue node list a optional variable.
#124
Kurt-Hetrick
opened
2 years ago
0
rework concordance workflow for hg19 and grch38 pipelines
#123
Kurt-Hetrick
closed
2 years ago
2
use dbSNP 129 for the TITV bed file variant metrics
#122
Kurt-Hetrick
closed
2 years ago
2
explicitly overwrite qc report stubs on every pipeline run
#121
Kurt-Hetrick
opened
2 years ago
0
place multiple library lists at the end of completed batch processing notification
#120
Kurt-Hetrick
closed
2 years ago
1
change gatk version for bqsr scripts in grch37 pipeline
#119
Kurt-Hetrick
opened
2 years ago
0
separate common scripts from build specific scripts.
#118
Kurt-Hetrick
closed
2 years ago
1
extract more cram headers and export to qc report
#117
Kurt-Hetrick
closed
2 years ago
1
add level in TEMP folder using time stamp
#116
Kurt-Hetrick
closed
2 years ago
1
split on _ for hapmap samples when doing concordance
#115
Kurt-Hetrick
closed
2 years ago
1
allow to write to subfolders
#114
Kurt-Hetrick
opened
2 years ago
1
updating picard tools version
#113
Kurt-Hetrick
opened
2 years ago
0
move temp files to sample subfolders
#112
Kurt-Hetrick
closed
2 years ago
1
remove scatter on genotype gvcfs
#111
Kurt-Hetrick
opened
2 years ago
0
adding threads variable
#110
Kurt-Hetrick
opened
3 years ago
0
switch over to gatk 4 docker/singularity containers
#109
Kurt-Hetrick
closed
2 years ago
1
sm tag sorting for creating qc report
#108
Kurt-Hetrick
closed
3 years ago
1
testing
#107
Kurt-Hetrick
closed
4 years ago
1
if input date is already ISO8601 then keep as is
#106
Kurt-Hetrick
closed
4 years ago
2
get rid of fix bam header in grch37 pipeline
#105
Kurt-Hetrick
closed
4 years ago
2
make some hack job for single end reads
#104
Kurt-Hetrick
closed
4 years ago
1
create pipeline for yale data
#103
Kurt-Hetrick
closed
4 years ago
2
add processing summary on README
#102
Kurt-Hetrick
closed
4 years ago
1
generate qc report when lab prep report is empty
#101
Kurt-Hetrick
closed
4 years ago
1
make qc report generator more robust: base distribution report
#100
Kurt-Hetrick
closed
4 years ago
1
make qc report generator more robust: mark duplicates
#99
Kurt-Hetrick
closed
4 years ago
1
experiment with coverage cap in collecthsmetrics
#98
Kurt-Hetrick
closed
4 years ago
11
fix holland qc reports stubs
#97
Kurt-Hetrick
closed
4 years ago
1
check to make sure that n+1 projects are not resubmitting a sample already released
#96
Kurt-Hetrick
opened
4 years ago
0
add FOLD_80_BASE_PENALTY to qc report
#95
Kurt-Hetrick
closed
4 years ago
1
fix file cleanup when sample sheet has multiple projects.
#94
Kurt-Hetrick
closed
4 years ago
1
create hg19 pipeline
#93
Kurt-Hetrick
closed
4 years ago
1
ignore novel ti/tv for successful completed runs requirement
#92
Kurt-Hetrick
closed
4 years ago
1
make qc report robust when pct base composition is not present
#91
Kurt-Hetrick
closed
4 years ago
1
sync gatk 4 versions between pipelines
#90
Kurt-Hetrick
closed
4 years ago
1
summarize workflow
#89
Kurt-Hetrick
closed
4 years ago
1
summarize software used
#88
Kurt-Hetrick
opened
4 years ago
0
summarize differences between grch37 and grch38 pipelines
#87
Kurt-Hetrick
closed
4 years ago
1
fix target bed file name after formatting
#86
Kurt-Hetrick
closed
2 years ago
2
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