cnnLSV: detecting structural variants by encoding long-read alignment information and convolutional neural network
git clone https://github.com/mhuidong/cnnLSV.git
python3, cv2, numpy, torch, torchvision, pysam, cigar
python cnnLSV.py <sorted.bam> <initial.vcf> <filtered.vcf> --dataset <real/sim> --model <simmodel.pt/realmodel.pt>
CnnLSV outputs the callset merged of several callers. This means that one SV may be detected by several callers. You can use the foolowing command to obtain unique result.
python cnnLSV_rmrd.py <multi.vcf> <unique.vcf>
HG00512, HG00513, HG00514, HG00731, HG00732, HG00733, NA19238, NA19239 and NA19240 datasets can be downloaded from:
HG002 CLR and HG002 CCS datasets can be downloaded from: