I'm generating synthetic reads to test a variant calling pipeline. SimulateReadsForVariants seems like a great tool, but the pipeline is designed to handle only pairs of Fastq files, not singletons.
Based on their position and orientation, it seems to me that the output reads are indeed paired, but there is nothing in the output BAM file to indicate which reads are paired. Currently, I am manually renaming apparent pairs of reads, but I would like a slightly less stupid and dangerous solution. Any ideas?
I would like to better understand how the module SimulateReadsForVariants is working with VCF files.
Given a VCF file containing 10 samples, I expected the SimulateReadsForVariants to simulate 10 BAM files for each sample. The module however simulates only 1 BAM file.
How can we generate sample-specific simulated BAM files?
Do we have to create 10 VCF files containing only 1 sample each?
Many thanks for your lights,