Simulation Tools To Generate Next-Generation Sequencing Reads along with their VCF

Question

[manojkumarbioinfo]

Hi,

I would like to simulate my read and i want to get both the read simulation and the positions of the simulated read in the form of VCF. I searched many tools but all the tools are simulating my reads but im not getting the vcf file.

can you suggest me some tools for read simulation along with their vcf file

[harold.smith.tarheel]

Simulated reads will not contain variants, unless they're generated from a sequence file that contains variants. You could create such a custom genome from a VCF plus reference genome with GATK's FastaAlternateReferenceMaker, then use BBMap's randomreads tool to create simulated data from the custom genome.

[Brian Bushnell]

I doubt you will find such a tool unless you write it yourself. And note that VCF files do not give positions of reads; they contain positions of variants. If you want the positions of the reads, you can use BBMap's randomreads.sh tool; it annotates each read with its genomic origin in the read header.

[manojkumarbioinfo]

Ya that what i'm trying i want to simulate the reads and i want their variant file where they have simulated.