Hi, I have CNV segment data from Sequenza for tumor-normal samples and CNV segment data from cnvkit for tumor-only samples. Can I combine these two …

Hello everyone, I am trying to run GISTIC from ASCAT segments, however,i am running into the following error. 1935 segment overlaps detected I read somewhere …

HI. I have downloaded the segment file from depmap portal (CCLE_segment_cn.csv) and the Segment_Mean column (relative copy ratio for that segment) seems somewhat different from …

I'm running GISTIC2 on Sequenza generated segmentation data from whole exome tumor-normal pairs. I keep encountering the following warning: ``` Warning: markers on largest gene …

Hi all, I am running Sequenza on some BAM files, but I keep getting this error: ``` [E::faidx_adjust_position] The sequence "NC_007605" not found ``` There …

I was trying to estimate the minimum sequencing depth required to confidently detect somatic variant using Poisson distribution based variant caller (such as somatic variant …

Hi everyone, I am trying to calculate the genomic relationship between discovery and target sample but I am not sure how to make the running …

From Sequenza output, there are following 13 columns, I am wondering which one I should use for GISTIC2 to calculate Set.CN? "chromosome" "start.pos" "end.pos" "Bf" …

I am using ExomeCNV to call copy numbers of some whole exome sequencing data (tumor and normal). I'd like to use GISTIC2.0 (standalone) to identify …

Hi, I have questions regarding [the CNV calls calculated from TCGA][1]. What I understand, they used a CBS algorithm to find segments which are changed …