Hi,
Is there a tool out there which will allow me, in any way, to determine how similar two fastq file sets (paired-end) are? It could be any metric like number of identical reads etc. or any other metric which can be relevant in this case.

I need this to diagnose the reason behind low agreement of variant calls between two identical runs: if the fastqs are quite similar to each other, then it was the variant-calling pipeline and not the upstream bench-work.

Thanks!
Maybe you could try [commet][1]? It was designed for metagenomics, but it allows you to compute a distance between two fastq files.


  [1]: https://colibread.inria.fr/software/commet/