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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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add base counts to the qc report
#37
Kurt-Hetrick
closed
6 years ago
2
handle both "-" and "/" as the delimeter for Run_Date in the sample sheet
#36
Kurt-Hetrick
closed
6 years ago
2
upgrade gvcf creation to gatk 4 eventually
#35
Kurt-Hetrick
opened
6 years ago
2
handle illumina demultiplexing/fastq architecture.
#34
Kurt-Hetrick
closed
5 years ago
2
output platform model to the qc report
#33
Kurt-Hetrick
closed
5 years ago
1
qc report. cmg.
#32
Kurt-Hetrick
closed
5 years ago
1
qc report: library name breakdown. sample not done at cidr.
#31
Kurt-Hetrick
closed
6 years ago
1
verifybamid2
#30
Kurt-Hetrick
opened
6 years ago
2
need to create dev branches
#29
Kurt-Hetrick
closed
5 years ago
1
things to convert for grch38
#28
Kurt-Hetrick
closed
5 years ago
5
exclude bigdata-03
#27
Kurt-Hetrick
closed
6 years ago
4
execute haplotype caller and per chromosome verifybamid sooner
#26
Kurt-Hetrick
closed
6 years ago
1
only write out time stats for jobs lasting more than 5 minutes
#25
Kurt-Hetrick
closed
6 years ago
1
find a way to have the qc report generate when only one sample is submitted
#24
Kurt-Hetrick
closed
3 years ago
1
delete all temp files automatically on a successful batch completion
#23
Kurt-Hetrick
closed
5 years ago
1
add titv bed file to ds tag
#22
Kurt-Hetrick
closed
6 years ago
1
send email when pipeline run is finished.
#21
Kurt-Hetrick
closed
6 years ago
1
fix command line outputs where appropriate
#20
Kurt-Hetrick
closed
6 years ago
1
cram.crai md5
#19
Kurt-Hetrick
closed
6 years ago
1
HS_LIBRARY_SIZE
#18
Kurt-Hetrick
closed
5 years ago
2
job arrays
#17
Kurt-Hetrick
opened
6 years ago
0
move all queue list determinations up to the top of submitter
#16
Kurt-Hetrick
closed
6 years ago
1
email
#15
Kurt-Hetrick
closed
6 years ago
1
handle old sample sheets...and possibly new?
#14
Kurt-Hetrick
opened
6 years ago
1
mark duplicates pixel distance setting
#13
Kurt-Hetrick
closed
5 years ago
2
look into implemented getopts/defaults/and interactive (case?)
#12
Kurt-Hetrick
opened
6 years ago
0
samtools 1+ ref cache for new users
#11
Kurt-Hetrick
closed
5 years ago
1
benchmark rare variants
#10
Kurt-Hetrick
closed
5 years ago
2
generate array for present chromsomes once for each unique bed files
#9
Kurt-Hetrick
closed
5 years ago
2
qc report: handle when verifybamid output is not generated
#8
Kurt-Hetrick
closed
6 years ago
1
demultiplexing
#7
Kurt-Hetrick
closed
5 years ago
1
automatically fix chr prefix in bed files if present for grch37 pipelines
#6
Kurt-Hetrick
closed
6 years ago
1
correctly grab the header of the cram file when the RG tags are in different order
#5
Kurt-Hetrick
closed
6 years ago
1
generating hash values for cram files
#4
Kurt-Hetrick
closed
6 years ago
1
bgzip/tabix final multi-sample vcf
#3
Kurt-Hetrick
closed
6 years ago
1
Platform model not added to CRAM header
#2
Kurt-Hetrick
closed
6 years ago
4
md5sum hash for gvcf
#1
Kurt-Hetrick
closed
6 years ago
1
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