vmukhina

BND representation

1

Hi @tjiangHIT, I used cuteSV to detect translocations in my sample and it seems that the output format differ from declared vcf4.2. According to the vcf specification https://samtools.github.io/hts-specs/VCFv4.2.pdf p5.4 each...

cnvkit access fails to add >NC* named regions to the .bed file

1

I run cnvkit access (0.9.9) on two files with the same fasta sequence labelled differently and I got different results: NC001526.4 was skipped whereas Nt_001526.4 was added to the output...

Hi, I am trying to compare SVs obtained from assembly and mapping approaches and use survivor to switch from Assemblytics_structural_variants.bed to .vcf and then to the .bedpe format. SURVIVOR is...

Hi, I am trying to install hicexplorer>=3.5 to use hicdetectloops function. Instructions work for mac but not for the Red Hat Enterprise Linux release 8.3 (Ootpa) ) where I anyway...

coverage inconsistency in sniffles v2

5

Hi, I performed kind of robustness test on my virus + human data by randomly subsampling reads and calling SVs with sniffles v2. Surprisingly, SV call for all reads miss...

error loading .hic file

6

Hi, I am trying to visualize file (~450mb) generated with juicer 1.6. It works seamlessly in web version but in desktop version (Juicebox 1.9.0, mac M1) it keeps evoking 'error...