neusomatic
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bioinform
NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection
Hi, friend when I install the software, it errors as this : Scanning dependencies of target seqan [ 5%] Creating directories for 'seqan' [ 10%] Performing download step (git clone)...
Hi, I got the truth_vcf . I want to train the data using the truth vcf by 5-fold-cross-validation analysis, and I got the dataset that including many files by 'process.py'....
Hi, @msahraeian I am wondering how did you deal with those multiallelic variants. If there is a site on genome with 3 or more alternate variant alleles meets the conditions...
I am currently working on a tumor bulk RNA-seq data set in order to identify somatic mutations. I have the BAM file for the tumor data set but I do...
Hi, I generated a training set comprising multiple samples using the method suggested in the README (using somaticseq's docker pipeline for bamsurgeon): https://github.com/bioinform/neusomatic#creating-training-data After training Neusomatic on this dataset, I...
Hi, I try to adapt your model for my deep-targeted sequencing data(> 100,000X depth) for somatic mutation calling. I noticed that the default read depth is identified as 100 in...
terminate called after throwing an instance of 'std::runtime_error' what(): cannot find index file for GRCh38.fa
If the number of threads is 1, additional threads/processes will not be spawned by avoiding use of multiprocessing pool.
Clang C/C++ configuration: { BasedOnStyle: Google, UseTab: Never, IndentWidth: 2, TabWidth: 2, BreakBeforeBraces: Attach, AllowShortIfStatementsOnASingleLine: false, IndentCaseLabels: false, AccessModifierOffset: -2, ColumnLimit: 90 }