Simulate Synthetic Reads with Structural Variants for a Given DGV

[fardokhtsadat]

Hello,

I would like to use VarSim to generate synthetic reads for structural variants from a given ground truth VCF file. To achieve this, I am using VarSim with the following parameters:

varsim/opt/miniconda2/bin/python varsim/varsim.py \
    --reference ref.fa \
    --sv_dgv fround_truth.vcf.gz \
    --id ID \
    --read_length 150 \
    --nlanes 1 \
    --simulator art \
    --simulator_executable varsim/opt/ART/art_bin_VanillaIceCream/art_illumina \
    --disable_rand_vcf \
    --sv_num_ins 0 \
    --sv_num_del 1 \
    --sv_num_dup 0 \
    --sv_num_inv 0 \
    --sv_percent_novel 0 \
    --sv_min_length_lim 20 \
    --out_dir results

However, this command raises the following error: ValueError: Need SV sequence file to fill in SV sequences

I think this error is because of missing --sv_insert_seq parameter. From the documentation, I can see that this argument is a file that contains the sequences to be inserted into the reads. I am wondering why this argument is required when a VCF file is provided to create the SVs from.

[yunfeiguo]

Hi please use --vcfs to supply VCF files. --sv_dgv only accepts the DGV format.