Comments (4)
raylim
commented on August 25, 2024
just fyi, github supports markdown (three single quotes are used to delimit code)
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charlottekyng
commented on August 25, 2024
This isn't done yet. Still need reference files for the breast panel v2 and exome and defaulting the optList$geneLocFile to the appropriate reference.
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charlottekyng
commented on August 25, 2024
Please fix this - I have 4 projects waiting for this fix. Thanks very much.
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charlottekyng
commented on August 25, 2024
Sorry i have to re-open this - the number of rows in the geneCN.txt file is smaller than the number of genes. Please print genes that cannot be assigned to segments. If there are genes for which positions cannot be retrieved, please check if they are the official gene names.
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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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