Kurt-Hetrick CIDR_SEQ_CAPTURE_JOINT_CALL issues

Kurt-Hetrick / CIDR_SEQ_CAPTURE_JOINT_CALL

CIDR exome and targeted resequencing joint calling/filtering pipeline

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performance: gather of pre refinement vcf is slow

#119 Kurt-Hetrick opened 1 month ago
1
K03A03-1_CONCORDANCE_ON_TARGET_PER_SAMPLE_ARRAY_38.sh

#118 Kurt-Hetrick opened 1 month ago
0
GRCH37/HG19 PIPELINES: CONCATENATE/COMBINE REJECTED LIFTOVER VARIANTS

#117 Kurt-Hetrick opened 1 month ago
2
do a gt array concordance in a single sge job

#116 Kurt-Hetrick opened 1 month ago
0
switch to doing concordance on grch38 arrays

#115 Kurt-Hetrick opened 4 months ago
2
implement vep for grch38 pipelines

#114 Kurt-Hetrick opened 5 months ago
0
validate that samples are not in two different projects in the sample sheet

#113 Kurt-Hetrick opened 9 months ago
0
combine liftover vcf might be bugged in grch38 pipelines

#112 Kurt-Hetrick closed 9 months ago
1
fix existence test for read group headers stub

#111 Kurt-Hetrick closed 9 months ago
2
decompress final reports if they have gone through the archiving pipeline

#110 Kurt-Hetrick closed 9 months ago
2
what if bed files are compressed.

#109 Kurt-Hetrick opened 9 months ago
1
qc report. enable reading in files that are compressed or not

#108 Kurt-Hetrick closed 9 months ago
2
qc report prep. single job instead of distributed across cluster.

#107 Kurt-Hetrick opened 10 months ago
0
validate bed files have proper contig names near beginning of submitters

#106 Kurt-Hetrick opened 11 months ago
0
combine liftover rejection vcf

#105 Kurt-Hetrick closed 11 months ago
1
add sanity checked to bgzipped final vcf versions

#104 Kurt-Hetrick closed 1 year ago
1
generalize multi-sample vcf names.

#103 Kurt-Hetrick closed 11 months ago
1
add optional arguments to change vqsr cut-offs.

#102 Kurt-Hetrick closed 10 months ago
1
restructure pipeline script organization

#101 Kurt-Hetrick closed 11 months ago
1
organize cmg and holland scripts

#100 Kurt-Hetrick closed 11 months ago
1
row number check for base distribution pct is not a number

#99 Kurt-Hetrick closed 11 months ago
1
update all pipelines

#98 Kurt-Hetrick closed 11 months ago
1
update mapping for hyb selection metrics

#97 Kurt-Hetrick closed 11 months ago
1
make std vqsr grch38 pipeline

#96 Kurt-Hetrick closed 2 years ago
1
remove hgmd from annovar reports

#95 Kurt-Hetrick closed 2 years ago
1
extract more cram headers and export to qc report

#94 Kurt-Hetrick closed 2 years ago
1
allow for vcf or final report as truth for gt concordance

#93 Kurt-Hetrick closed 1 year ago
1
do a qc report prep in a single sge job

#92 Kurt-Hetrick closed 2 years ago
1
send teams notification if snp vqsr fails once

#91 Kurt-Hetrick closed 2 years ago
1
allow for multiple bait, target, titv bed files for non-cmg projects

#90 Kurt-Hetrick opened 2 years ago
1
set a cut-off for number of samples to perform automatic qc report generation

#89 Kurt-Hetrick opened 2 years ago
1
exit when there is no final report

#88 Kurt-Hetrick closed 2 years ago
1
liftover needs a lot of memory

#87 Kurt-Hetrick closed 2 years ago
1
change vcf header for AS_ info annotations.

#86 Kurt-Hetrick closed 2 years ago
2
create a slimmed down by family coverage report

#85 Kurt-Hetrick closed 3 years ago
1
update EnhancedSequencingQCReport.jar

#84 Kurt-Hetrick closed 3 years ago
1
gatk selectvariants 4.1.9.0

#83 Kurt-Hetrick closed 3 years ago
1
switch over to gatk 4 docker/singularity containers

#82 Kurt-Hetrick opened 3 years ago
0
capture exit signal from enhancedqcreport.jar

#81 Kurt-Hetrick closed 3 years ago
1
make qc report job dependency more robust

#80 Kurt-Hetrick closed 2 years ago
1
testing

#79 Kurt-Hetrick closed 3 years ago
1
investigate difference in snp count per sample between hg19 and grch37

#78 Kurt-Hetrick closed 4 years ago
1
make qc report generator more robust: base distribution report

#77 Kurt-Hetrick closed 4 years ago
1
make qc report generator more robust: mark duplicates

#76 Kurt-Hetrick closed 4 years ago
1
generate multi-sample vcf metrics for release

#75 Kurt-Hetrick closed 2 years ago
3
add FOLD_80_BASE_PENALTY to QC report

#74 Kurt-Hetrick closed 4 years ago
1
create hg19 pipeline

#73 Kurt-Hetrick closed 4 years ago
1
wall clock tracker

#72 Kurt-Hetrick closed 1 year ago
1
histogram of prop of het genotypes by ab for het for deletions ge 10, af ge 20

#71 Kurt-Hetrick closed 1 year ago
1
look at contamination vs number of AB freq gt than 0.9 calls

#70 Kurt-Hetrick closed 1 year ago
2