Accucopy
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polyactis
Accucopy is a computational method that infers Allele-Specific Copy Number alterations from low-coverage low-purity tumor sequencing data.
Hello working with several samples, all but 1 sample output the cnv.output.tsv. Have ran accucopy on this single sample many times, however no CNV output. Accucopy finishes with no error....
The web site https://www.yfish.org/display/PUB/Accucopy referenced here is broken
Hi, I want to use Accucopy on long read data, such as Pacbio or Nanopore. So I want to ask, whether your model fits long reads data or not. If...
Hi, I'm getting the following error while trying to run accucopy with various samples : _" 5_1] [plot_model_select] IOError: Unable to open file (unable to open file: name = '/data/modif_genome_test1/model_selection_l...
Hi @polyactis, First, thank you for this great tool. I aligned my reads to the reference genome included in `hs38d1` provided by `Accucopy` and sorted the bam files with duplicates...
Hi there, thank you for developing accucopy. it was relatively straight forward to run and fast! How do we prepare input for pyclone-vi (example: https://github.com/Roth-Lab/pyclone-vi/blob/master/examples/tracerx.tsv) from `cnv.output.tsv`? Specifically, how do...
Hi there, Hope you're well! I am running accucopy on multiple paired tumour-normal WGS samples. It has worked perfectly on most of them, except for in one sample where the...
Hi Thanks for this excellent tool. caller_path the path of the 3rd-party variant calling program; in demo, Strelka2 was used. could gatk be uesd as caller?
Dear author, Thanks for developing this software. I re-aligned my bam files with the provided reference genome, then ran Accucopy docker image with Singularity following the instructions, but I always...
Hi, I tried the new mode "--period" option and found small bug in the main.py script at line 540. It shows "period" parameter not defind. To fix this, I just...
