Comments (1)
filtered positions with GMAF > 0.01 if --novel flag is set (which is also set by default)
from modules.
Related Issues (20)
- need to check for mapped reads to all the targeted contigs HOT 1
- igvtools index fails occasionally/intermittently HOT 5
- integration test for variant calling
- mutect2 workflow
- fix the variant tests
- split pathogenicity annotation up for SNPs and indels
- pathogenicity requires a few minor fixes
- pathogenicity missing for missense mutations
- mutation taster query default result should be passenger
- facets annotations missing for vcfs where chromosome=X
- pathogenicity calling of inframe sites
- facets LOH true/false
- empty/invalid VCF files are occasionally generated
- merge multiple indel call variants, take variants present in at least 2
- oncokb annotation
- annotate only variants in vcf that PASS
- annotate fuentes and dgd
- Update hotspot annotation based on Chang et al. 2017
- Pipeline broken HOT 1
- modules/copy_number/ntaiscore.R HOT 1
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from modules.