Tweet
Hi, I tried to use VarSim pipeline to generate reads (using ART). The steps for randvcf2vcf, randdgv2vcf, vcf2diploid and art read simulator etc. are all fine, however the fastqliftover gives errors. I'm not very familiar with java but I tried to dig into source code at: https://github.com/bioinform/varsim/...qLiftOver.java
It seems to me that fastqliftover does not support single-end reads, but I'm not sure. I also tried to create empty .fq and .aln files for a second read file, to be coupled with the simulated single-end read, and try to "fool" the tool but not successful.
Can anyone help to confirm or give me a hint how to simulate single-end reads using VarSim pipeline? Thanks.
It seems to me that fastqliftover does not support single-end reads, but I'm not sure. I also tried to create empty .fq and .aln files for a second read file, to be coupled with the simulated single-end read, and try to "fool" the tool but not successful.
Can anyone help to confirm or give me a hint how to simulate single-end reads using VarSim pipeline? Thanks.