Reads covered by variants

[ranijames]

Hello All,

This is not an issue, but I have a technical question. I wanna find the reads covered by each variant in the simulated truth VCF file. And I do not wanna do any secondary analysis for that (for example, using another variant caller on the fastq files) this is to avoid any bias from the secondary analysis tools. I wanna get the reads mapped or covered to each variant in the VCF file. Usually, the VCF file has the DP4 field where we get the number of reads covered. The simu.truth.vcf file from the Varsim tool, however, does no has such field, other than SVLEN. I have read the paper and supplementary papers a couple of times, but could not find any information. In this case, I would like to know if there any potential output files from which I can get this information.

Thank you

[yunfeiguo]

Hi @ranijames sorry we don't have a tool for this purpose yet.