Kurt-Hetrick CIDR_WES issues

Kurt-Hetrick / 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