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Kurt-Hetrick
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CIDR_SOMATIC_WES_PIPELINES
currently for paired tumor - normal WES samples processed with TWIST UMIs
MIT License
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create notification system for when demultiplexing has completed.
#20
Kurt-Hetrick
opened
1 year ago
1
newer picard versions have "too many file open" issues with demultiplexing
#19
Kurt-Hetrick
opened
1 year ago
2
dynamically create sample sheet from qc report for paired tumor, normal calling
#18
Kurt-Hetrick
opened
1 year ago
0
impure normal vs pure panel of normals to used for calling
#17
Kurt-Hetrick
opened
1 year ago
0
CreateSomaticPanelOfNormals
#16
Kurt-Hetrick
opened
1 year ago
0
evaluate gatk matched contamination tools for paired calling pipeline
#15
Kurt-Hetrick
opened
1 year ago
0
combine germline calls with somatic calls
#14
Kurt-Hetrick
opened
1 year ago
0
add gatk getpileupsummaries and calculatecontamination
#13
Kurt-Hetrick
closed
1 year ago
1
evaluate gatk calculatecontamination
#12
Kurt-Hetrick
closed
1 year ago
1
change unmapped bam files to unmapped cram files
#11
Kurt-Hetrick
opened
1 year ago
1
evaluate FilterSomaticVcf from fgbio
#10
Kurt-Hetrick
opened
1 year ago
0
add bed file names to qc report
#9
Kurt-Hetrick
closed
1 year ago
2
output READ_STRUCTURE and illumina SS in submission notification
#8
Kurt-Hetrick
closed
1 year ago
1
make read structure argument optional instead of mandatory
#7
Kurt-Hetrick
opened
1 year ago
1
does mutect2 need bam files as input
#6
Kurt-Hetrick
closed
1 year ago
1
compare umi-aware dup pipeline to idt pipeline
#5
Kurt-Hetrick
opened
1 year ago
0
can demux be part of overall qc pipeline
#4
Kurt-Hetrick
opened
1 year ago
2
profile ExtractIlluminaBarcodes and IlluminaBasecallsToSam
#3
Kurt-Hetrick
opened
1 year ago
3
read structure populated from runParameters.xml
#2
Kurt-Hetrick
closed
1 year ago
2
aggregation in cloud
#1
Kurt-Hetrick
closed
1 year ago
1
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