GACGAMA

I'm segmenting my files with a vcf, with cnvkit version 0.9.11 from conda I'm getting the following error with the segment command: ``` Segment chr1:258166-121975959 on allele freqs for 91...

Hello everyone! I've called my segments by using both a VCF with tagged somatic/germline variants, exported to theta2 and and imported back to CNVkit. Now I need to export the...

Hello! After reviewing the full documentation, I got a question that was not clear on it: Lets say I'm analyzing a cohort of tumor-normal samples, but I also have available...

Controls / cases counts inverted when using binary model

7

Hello! I've finished analyzing a large cohort using 0/1 numerical values for control/case status respectively. Then I went to my vcf to count the distributions of variants for each group....

AnnotSV passing wrong arguments to variant convert

5

Hello! I'm using variantconvert 2.0.1 and the latest AnnotSV within a conda installation. When generating MANTA annotations, tsv files are produced correctly with: `AnnotSV -SvinputFile file1.vcf -annotationsDir /scratch4/nsobrei2/references/annotsv/AnnotSV_annotations/ -genomeBuild GRCh38...