feat: Somatic cnv checking #426
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fix: added vcf indexation & md5 checksums feat: remove possibility of running script without CNV bed file (should be done in Snakefile/workflow) refactor: make black happy
…esence of multiple tumors
mbenary
requested changes
Aug 21, 2023
| excluded_regions: "" # Bed file of regions to be excluded | ||
| max_depth: 10000 # Max depth for pileups | ||
| min_cov: 20 # Minimum depth for reference and alternative alleles to consider variant | ||
| min_baf: 0.4 # Maximum BAF to consider variant as heterozygous (between 0 & 1/2) |
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variable name and comment not consistent. Please adjust.
| y <- read.table(cnv, sep="\t", header=0) | ||
| colnames(y) <- c("CHROM", "start", "stop", "name", "LFC", "strand") | ||
| y <- y |> | ||
| dplyr::mutate(LFC=replace(LFC, strand == "-", LFC[strand=="-"])) |> |
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This is not changing anything, Add "-" in front of replacement.
This was referenced Dec 9, 2024
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At the moment, implementation of steps
somatic_wgs_cnv_calling&somatic_targeted_seq_cnv_callingare based on coverage depth only. From that coverage, the log ratio of tumor to normal samples depth is computed, and after segmentation, the expected number of alleles in the tumor is computed.To check quality of the log fold change of depths and the allele number call, the
somatic_cnv_checkingstep is organized in the following way:Remains to be done: