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hg19 runvar bin bug for 1Mb #109
Description
Hi,
I noticed that when running runvarbin with Hg19 ref genome and 1Mb resolution, the function splits bins into 220kb size windows (as I get 12205 bins) at the end of this step. Here is an example:
tumor <- runVarbin("/path/to/clean_bam/", genome = "hg19", resolution = "1Mb", min_bincount = 10, remove_Y = FALSE, is_paired_end = TRUE)
tumor
class: CopyKit
dim: 12205 7339
metadata(3): genome resolution vst
assays(6): bincounts ft ... ratios logr
rownames(12205): 1 2 ... 12204 12205
rowData names(7): bin_length gene_count ... abspos arm
colnames(7339): AAACGAAAGATTAGAC-1.filtered.sorted AAACGAAAGCGTCAAG-1.filtered.sorted ...
TTTGTGTTCGATAGCT-1.filtered.sorted TTTGTGTTCTACATCT-1.filtered.sorted
colData names(15): sample reads_assigned_bins ... cell_corr_value outlier
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
rowRanges has: 12205 ranges
Phylo: Phylogenetic tree with 0 tips and nodes
consensus dim: 0 0
Could you please fix this in the source code?
Thanks!
Activity
darlanminussi commentedon Sep 26, 2025
@Kris69w Could you take a look at this?
Kris69w commentedon Oct 14, 2025
Hi, right now different genome resolution is only available for the hg38 genome. we will work on adding genome resolution scaffold other than 220kb for hg19.
Thanks!