cnv_facets
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dariober
Somatic copy variant caller (CNV) for next generation sequencing
The position of the output from snp-pileup is one-base, so the start position in facetsRecordToVcf should not "+1".
Hi, I have some human cell line data whose original ploidy is not 2n. In fact, it is 4n. Is there any way to force the ploidy to this value...
Hi, I was wondering if there is a threshold I could use on the log-odds-ratio (MAF) value to call a region as LOH? I am calculating the converted MAF_R as...
Hi @dariober, I've been trying to troubleshoot cnv_facets.R (thank you btw) but i'm always stuck after the pile up files have been generated. I've posted on Biostar and people seem...
Hello, Thanks for the facets wrapper. We have been stored alignment files with CRAM format. Would it possble to support CRAM format? Best, Ya
Hello, Thanks for the facets wrapper. We have 23 unmatched control bam files. I would like to utilize them as a single unmatched controls against tumor samples. I can merge...
Hi Dario, Would it be possible to add an option to run only the SNP-pileup step with _--snp-nprocs_ ? This would only generate the pileup input for option 2. The...
The error I am getting is this - akhileshmishra@IMS-549548-IN-AMIRSHRA-iMac-27 ~ % conda create -n cnv Collecting package metadata (current_repodata.json): done Solving environment: done -## Package Plan ## environment location: /Users/akhileshmishra/miniconda3/envs/cnv...
Hi Dariober when I run with unmatched mode (the unmatched bam are merged from 10 un-related normal samples) cnv_facets.R \ -t ./bams/S21-096.bam \ -n merged_normal.bam \ --unmatched \ -vcf vcfs/S21-096.hard-filtered.vcf.gz...
I've attempted to install cnv_facets package using: ``` conda create -n facets conda activate facets conda install -c bioconda -c conda-forge cnv_facets ``` It's taking forever to install and is...
