nickhsmith edfe28a5e0 Variant recalibration (#1885) ... * update tests * update * update * make the manta inputs consistant for germline/somatic/tumoronly * match chromosomes to cram file (chr21) * undo genotypegvfs * undo genotypegvfs * update VariantRecalibrator * lint * add '--resource:' tag Co-authored-by: Smith Nicholas <smith@in.tum.de> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>		2022-07-15 09:21:34 +02:00
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applybqsr
applybqsrspark	similar issues arise with bqsrspark, also use broadinstitute container	2022-06-09 15:29:00 +02:00
applyvqsr
baserecalibrator
baserecalibratorspark	similar issues arise with bqsrspark, also use broadinstitute container	2022-06-09 15:29:00 +02:00
bedtointervallist
calculatecontamination
calibratedragstrmodel
cnnscorevariants
combinegvcfs
composestrtablefile
createsequencedictionary
createsomaticpanelofnormals
estimatelibrarycomplexity
fastqtosam
filtermutectcalls
filtervarianttranches
gatherbqsrreports	Improve descriptions for modules with missing	2022-07-06 12:03:08 +02:00
gatherpileupsummaries
genomicsdbimport
genotypegvcfs
getpileupsummaries	GATK/Getpileupsummaries: If no intervals use variants instead (#1787)	2022-06-16 15:00:01 +02:00
haplotypecaller	added dragstr model to haplotypecaller	2022-06-02 14:08:09 +02:00
indexfeaturefile
intervallisttobed
intervallisttools
learnreadorientationmodel
leftalignandtrimvariants	Add module: gatk4/leftalignandtrimvariants (#1808)	2022-06-28 10:44:08 +02:00
markduplicates
markduplicatesspark	remove singulairty container	2022-06-09 15:16:11 +02:00
mergebamalignment
mergemutectstats
mergevcfs
mutect2
reblockgvcf	Update modules/gatk4/reblockgvcf/main.nf	2022-06-09 15:11:18 +02:00
revertsam
samtofastq
selectvariants
splitintervals
splitncigarreads
variantfiltration
variantrecalibrator	Variant recalibration (#1885)	2022-07-15 09:21:34 +02:00