Low Complexity region determination using SEG - Biostar: S That will compile a binary called seg, which will tell you the options if you run it without any arguments It works in two general modes: 1) masking low-complexity region with X characters if you supply the -x switch; 2) showing low-complexity regions on the left and normal complexity regions on the right
How to draw heatmap plot use cnv seg data called by gatk? - biostars After command ModelSegments we can get seg data and plot use PlotModeledSegments, this give CNV plot for each sample I have many samples(100+) and want to generate a heatmap to see what's differentce( common) between samples
How to import the output of CNVkit into GISTIC2. 0 - biostars The segmentFile is just SEG format, so you can do cnvkit py export seg * cns -o gistic segments to generate it For the markerFile, see Luca's notes in the linked issue I think you can use the first 3-4 columns from cnvkit py export jtv to get most of the way there
How to convert my files (cnv seg, refseq) to . bed format The general answer here is that these are all tabular formats, so you can extract the columns you need using standard Unix tools or a short script in R or Python The format of BED is chromosome start end, while the UCSC RefSeq table and and the SEG format both have these columns along with others
Interpreting GISTIC2 output - Biostar: S seg CN data in input seg file is log2(copy number) - 1, so you need to convert data from "all_lesions" file back to raw copy number "actual copy number" of the first sample in your example data is "-0 57388" then you can get raw copy number by:
Understanding GISTIC 2. 0 - Biostar: S I have 58 samples of whole genome sequencing data with the seg copy number file I prepared the input for gistic as stated in the literature and the forum: a txt file with 6 columns: sample, chromosome, start, end, marker and seg CN
bcftools mpileup sample labels, seg fault - Biostar: S Running this kind of command gives seg fault: bcftools mpileup -s sample1,sample2 -f genome fasta sample1 bam sample2 bam However this works (without -s): bcftools mpileup -f genome fasta sample1 bam sample2 bam bcftools 1 7 Using htslib 1 7-2 Any ideas why this could be? Thanks, Gregor
Meaning of TCGA CNV data - Biostar: S If you check the full names of the files you refer to you can see that they contain either "grch38 seg" or "nocnv grch38 seg" The first is a segmented (see papers in my answer) copynumber profile mapped to the hg38-build of the human genome and the second is the same but filtered for CNV's (normally occurring Copy Number Variant's != tumor
Tutorial: Analyze exome Copy number variation (CNV) in . . . - biostars But since GISTIC need segmentation file and marker file which require number of markers to be filled in the segmentation file and the marker position in the marker file Seg CN i can get from the CNV segments from CNVnator So, was thinking if CNVnator output provides these information
Why does GISTIC require a markers file? - Biostar: S Segmented copy numbers ( seg file, e g CBS output) Gene annotation file in GISTIC format (refgene file) A markers file that gives the genomic position of probes windows that was used (before segmentation) I wonder what GISTIC does with the markers file does and why it is required