VarSim: Large structural variants (DELs) are not simulated.

[bioinfo89]

Hi,

I want to simulate only deletions on chromosome 22, between range 1-30 bps and 30bps to 1Mb. For the same I am using the following command:

python varsim.py --vc_in_vcf All_20170710_chr22_variants_final.vcf --sv_dgv GRCh37_hg19_supportingvariants_2013-07-23_wdchr.txt --reference hg19/chr22.fa --id Simchr22 --read_length 125 --mean_fragment_size 500 --sd_fragment_size 100 --sv_num_ins 0 --sv_num_dup 0 --sv_num_inv 0 --vc_num_del 10 --sv_num_del 5000 --sv_percent_novel 0.2 --vc_percent_novel 0.01 --vc_min_length_lim 1 --vc_max_length_lim 29 --sv_min_length_lim 50 --sv_max_length_lim 1000000 --nlanes 1 --total_coverage 30 --simulator_executable art_bin_MountRainier/art_illumina --out_dir chr22 --log_dir log --simulator art --profile_1 art_bin_MountRainier/Illumina_profiles/HiSeq2500L125R1.txt --profile_2 art_bin_MountRainier/Illumina_profiles/HiSeq2500L125R2.txt --varsim_jar VarSim.jar --java_max_mem 35g

The output vcf file only has small DELs and the random sv VCF is empty. The vcf2diploid.out is also empty.
Please find attached the varsim.log for your reference.

It looks like the input DGV file format might be causing the error since it is skipping most of the variants (as per the RandDGV2VCF.err). But I am not sure how to go about it.

Any help would be highly appreciated. Thank you!

varsim.log