varsim
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bioinform
VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications
Hello, I'm running VarSim 0.6.3, and when I run the Varsim.jar vcfcompare tool, I'm getting weird artifacts in my output VCF files. For example: In my False Negative set, I...
I'm having trouble reading any kind of bam file into SAMcompare. This is from a bam file generated by ART. ``` VarSim 0.5.3 21 Apr 2016 00:28:03,394 INFO [main] (SAMcompare.java:175):...
Depending on the desired number of lanes, a large number of threads can be launched which may overwhelm the system. Especially if [ number of lanes ] >> [ number...
Hello, I ran VarSim V0.5.2 with the script that had worked well with V0.5.1, and the output tumor vcf file tumor_somatic.vcf has no variant. Could you check this? Thanks, Yun
Hi, I've been using VarSim to simulate reads for alignment, and would like to compare the alignment accuracy before secondary analysis. I'd like to test with single-end reads. However fastqLiftover...
Bumps [jackson-databind](https://github.com/FasterXML/jackson) from 2.9.10.4 to 2.13.4.1. Commits See full diff in compare view [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter...
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hi,I'm using varsim_somatic(docker:rssbred/varsim),I got cosmic_somatic.vcf has no variant. My command is : /opt/varsim/varsim_somatic.py --reference ref_out/my_ref.fasta --id cosmic --som_num_snp 20 --som_num_ins 20 --som_num_del 20 --som_num_mnp 20 --som_num_complex 20 --cosmic_vcf CosmicCodingMuts_COSMICv96.vcf.gz --normal_vcf...
Thank you for sharing the varsim. I was testing it, I found in line 134 of varsim_somatic.py,the run_randvcf function should have 9 arguments, you only wrote 8,you missing the sample...
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Bumps [htsjdk](https://github.com/samtools/htsjdk) from 2.14.3 to 3.0.1. Release notes Sourced from htsjdk's releases. 3.0.1 Fix for a long standing vulnerability around temporary directory creation which could expose data to malicious users...