Kurt-Hetrick CIDR_SOMATIC_WES_PIPELINES issues

Kurt-Hetrick / CIDR_SOMATIC_WES_PIPELINES

currently for paired tumor - normal WES samples processed with TWIST UMIs

MIT License

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issues

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run somatic vcf metrics on coding/titv bed file

#70 Kurt-Hetrick opened 2 months ago
0
CALCULATE BARCODE SUMMARY METRICS

#69 Kurt-Hetrick opened 4 months ago
2
investigate haplotype caller gvcf contamination allele fraction cut-off

#68 Kurt-Hetrick opened 4 months ago
0
generate cidrseqsuite samplesheet from paired samplesheet in paired calling pipeline

#67 Kurt-Hetrick opened 4 months ago
0
bug/feature enhancement to qc report generated solely on sample sheet

#66 Kurt-Hetrick opened 4 months ago
0
make paired caller more robust to whether or not bed file name in sample sheet has .bed extension or not

#65 Kurt-Hetrick closed 4 months ago
1
combine barcode metrics output per flow cell

#64 Kurt-Hetrick opened 5 months ago
0
allow number of no calls and mismatches allowed to be changed

#63 Kurt-Hetrick closed 2 months ago
1
summarize barcodes seen and delete files

#62 Kurt-Hetrick closed 2 months ago
1
add another lookup path for folder lookup in demuxing

#61 Kurt-Hetrick closed 2 months ago
1
dynamically set computational resources request based on how many lanes are in cidr samplesheet

#60 Kurt-Hetrick opened 5 months ago
0
remove fgbio and the need of an iem samplesheet

#59 Kurt-Hetrick closed 5 months ago
1
bugs in grch37 qc pipeline

#58 Kurt-Hetrick opened 7 months ago
0
switch to doing concordance on grch38 arrays

#57 Kurt-Hetrick closed 7 months ago
1
investigate end tasks execution

#56 Kurt-Hetrick opened 9 months ago
0
add mate flags/run samblaster for umi workflow?

#55 Kurt-Hetrick opened 10 months ago
0
create a non-umi version

#54 Kurt-Hetrick closed 9 months ago
1
reconfigure mutect2 calls/filtering

#53 Kurt-Hetrick opened 10 months ago
0
benchmark tumor only vs tumor/normal calls

#52 Kurt-Hetrick opened 10 months ago
0
compress barcode.txt

#51 Kurt-Hetrick closed 5 months ago
2
submission notification. how many lanes were submitted

#50 Kurt-Hetrick opened 11 months ago
0
assumption: need to generate sample sheet during paired calling to feed ben's enhanced qc report

#49 Kurt-Hetrick closed 10 months ago
1
evaluate gatk 4.5.0.0

#48 Kurt-Hetrick opened 11 months ago
0
another test

#47 Kurt-Hetrick closed 12 months ago
0
test

#46 Kurt-Hetrick closed 12 months ago
1
add allele fraction cut-off to notifications

#45 Kurt-Hetrick closed 11 months ago
1
allow demuxing to use run folders from the novaseqx

#44 Kurt-Hetrick closed 1 year ago
1
novaseqx fastq look up

#43 Kurt-Hetrick closed 1 year ago
1
LIMITATION: initial paired calling pipeline

#42 Kurt-Hetrick opened 1 year ago
0
validate that there are no somatic variants from the normal in mutect2 output vcf metrics

#41 Kurt-Hetrick opened 1 year ago
0
make sure qc pipelines are in sync

#40 Kurt-Hetrick closed 11 months ago
1
validate that bed files exist

#39 Kurt-Hetrick opened 1 year ago
0
CollectVariantCallingMetrics bed files. 1 or 0 based.

#38 Kurt-Hetrick opened 1 year ago
1
there should only be one unique bed files per type (bait, target, etc) in input manifest

#37 Kurt-Hetrick opened 1 year ago
0
REMINDER: query normal metadata from qc report from base subject id

#36 Kurt-Hetrick closed 11 months ago
1
bed files will need to be in predetermined location as of right now

#35 Kurt-Hetrick opened 1 year ago
1
build in validation that there is only 1 tumor type per individual in qc report

#34 Kurt-Hetrick closed 11 months ago
3
add 100x to coverage reports

#33 Kurt-Hetrick closed 1 year ago
1
populate tumor and normal sample name fields in maf

#32 Kurt-Hetrick closed 11 months ago
1
collapse all bed files before calling

#31 Kurt-Hetrick opened 1 year ago
0
build in allele freq filter parameter for paired calling in submission

#30 Kurt-Hetrick closed 11 months ago
1
paired tumor/normal calling pipeline: perform normal tumor concordance

#29 Kurt-Hetrick closed 11 months ago
1
remove mito chrom from aneuploidy check report

#28 Kurt-Hetrick opened 1 year ago
0
fix header in per chromosome verifybamid report

#27 Kurt-Hetrick opened 1 year ago
0
mutect filter output statistics

#26 Kurt-Hetrick opened 1 year ago
0
mutect2 vcf output

#25 Kurt-Hetrick opened 1 year ago
1
COSMIC investigation/integration

#24 Kurt-Hetrick opened 1 year ago
0
reference sort bed files

#23 Kurt-Hetrick opened 1 year ago
0
add coverage metrics over 100x to qc report

#22 Kurt-Hetrick opened 1 year ago
1
change haplotype caller contamination adjustment from freemix to gatk tumor contam

#21 Kurt-Hetrick opened 1 year ago
1