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bioinform
VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications
Hello, I was wondering if there is a way to control how many clipped reads are simulated via Varsim (or Art). Many thanks Jorge
Hello @yunfeiguo I'm trying to replicate the generation of fastqs using varsim_multi.py and i keep getting stuck towards the end: here is the command i used: `python /Public/varsim/master/varsim/varsim_multi.py --regions /DGD/Research/ConsPanel_RD/SIM/CONS.bed...
Hello @yunfeiguo I was able to successfully run varsim_multi.py and generate fastq with variants "spiked in" from dbsnp snps. However, the coverage of the samples looks very funky! see how...
Hi, I'm trying to run Varsim_multi.py on hg19, using a BED file of exonic regions I downloaded from ucsc table browser. I'm using java version "1.8.0_131" Java(TM) SE Runtime Environment...
Hi, I want to disable read simulation by using --disable_sim, but it still asked for simulator_exectuable path. Do you have any suggestions about this? Thank you, Tingting
Hi, I have a problem where VarSim 0.8.2 (public release) adds only insertions and duplications. I tried to find a problem in command line, or used dgv file, but couldn't....
Hi Developers, How to set the Varsim parameters to simulate a single-end file of shallow whole-genome sequencing (0.5x) given mean fragment size of 167 bp? Best Pitithat
right now copy number loss is ignored, we probably should add it back. https://github.com/bioinform/varsim/blob/master/src/main/java/com/bina/varsim/util/DGVparser.java#L157
Hello ,sorry for bother your again,i'm using varsim_multi.py to get simulated data,here is my command: `python /gpfs/users/yanghao/software/varsim/varsim_multi.py --regions ../Euler_MSKCC_actionable_cancer_original.sort.bed --sv_insert_seq /gpfs/users/yanghao/software/varsim_run/insert_seq.txt --sv_dgv /gpfs/users/yanghao/software/varsim_run/GRCh37_hg19_supportingvariants_2013-07-23.txt --reference /gpfs/users/yanghao/database/ref/b37/human_g1k_v37_decoy.fasta --vc_num_snp 3000000 --vc_num_ins 100000 --vc_num_del...
