varsim
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bioinform
VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications
Hi,there,i'm using varsim to create a simulated somatic data,and i hava a error message,like below: `python varsim_somatic.py --reference /gpfs/users/yanghao/database/ref/b37/human_g1k_v37_decoy.fasta --id cosmic --som_num_snp 10000 --som_num_ins 2000 --som_num_del 2000 --som_num_mnp 200 --som_num_complex...
Hi yunfeiguo , as title, I want to simulate CNVs in WES data Is this tool able to simulate variant in WES mode?
Hi there! I'm trying to make a somatic simulation. First, I have simulated germline data as suggested: `python varsim.py --vc_in_vcf All.vcf.gz --reference hs37d5.fa --sv_insert_seq insert_seq.txt --sv_dgv GRCh37_hg19_supportingvariants_2013-07-23.txt --id simu --read_length...
Hi, I have a couple of questions. 1) When I simulate variants I usually do not get the required number. e.g. --sv_num_del 5000 --sv_num_inv 5000 yields ~3500 deletions and ~700...
This will allow to limit the amount of parallelism which gets used. Also, add some options to limit memory usage.
Hi, I found two bugs when repeating the varsim example. ``` File "/opt/varsim-0.7.10/varsim.py", line 458, in varsim_main simulator_commands_files.append((art_command, os.path.join(log_dir, "art.lane%d.out" % (i)), os.path.join(log_dir, "art.lane%d.err" % (i)))) NameError: global name 'art_command'...
The reference sequences from varsim has two sequences (paternal and maternal), and the name is same in the normal sample and the tumor sample. Sometimes, I have to use these...
- [x] [RES-552](https://binatechnologies.atlassian.net/browse/RES-552) - [x] Blocking PRs: ADD HERE IF ANY * People - [x] Reviewers (>=1): @marghoob - [x] Merger (>=1): @marghoob - [x] FYI: @ulitskyb - [x] Release...
Hi @johnmu, Happy new year! Hope you had a great vacation with your baby! I wonder if you would like to keep the branches you created (other than master and...