VarSim 0.8.2 fails to add INV, DEL

[Chandralinjo]

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. Is this a known issue, or am I missing something in the command line?

I am attaching varsim.log file, and resulting sv.vcf.stats file.

Command line: export _JAVA_OPTIONS="-Xmx90000m" && python /opt/VarSim-0.8.2/varsim.py --reference /sbgenomics/Projects/9f720c02-7ff8-4696-9e44-33f79ec33f97/human_g1k_v37_decoy.fasta --seed 20160320 --id VarSim_3200_RND --read_length 150 --nlanes 8 --total_coverage 30 --mean_fragment_size 360 --sd_fragment_size 50 --vc_num_snp 1000000 --vc_num_ins 0 --vc_num_del 0 --vc_num_mnp 2000 --vc_num_complex 10000 --vc_percent_novel 0.02 --vc_min_length_lim 1 --vc_max_length_lim 49 --vc_in_vcf /sbgenomics/Projects/9f720c02-7ff8-4696-9e44-33f79ec33f97/All_20161121.vcf --vc_prop_het 50 --sv_num_ins 800 --sv_num_del 800 --sv_num_dup 800 --sv_num_inv 800 --sv_percent_novel 0.05 --sv_min_length_lim 50 --sv_max_length_lim 200000 --sv_insert_seq /sbgenomics/Projects/9f720c02-7ff8-4696-9e44-33f79ec33f97/insert_seq.txt --sv_dgv /sbgenomics/Projects/9f720c02-7ff8-4696-9e44-33f79ec33f97/GRCh37_hg19_supportingvariants_2013-07-23.txt --simulator_executable /opt/VarSim-0.8.2/ART/art_bin_MountRainier/art_illumina

Thanks!

[yunfeiguo]

Hi @Chandralinjo this is a known issue in varsim. We will work on it. Thanks!

[CodingKaiser]

Are there older versions of this not affected by this bug? Or is it just 0.8.2 and 0.8.3?

[yunfeiguo]

Hi, this issue affects both current and previous versions. Thanks.