Single-end support

[Rubbert]

The ATAC-seq data we work with is single-end, which is not supported at the moment. Ideally, of course, this feature could be introduced. However, in the meantime, I was wondering if this is still true if I provide aligned BAM files and we do the peak calling ourselves? If I skip those steps, will VarCA be able to handle single-end data?

Thanks!

[aryarm]

Hi @Rubbert,

Yes, VarCA was built and tested with paired-end reads, but in theory, it should be possible to coerce it into using single-end reads if you skip the peak calling step! The only steps that are specific to the paired-end reads occur before the peak calling.

If you don't mind, I would be very interested to hear about how this goes! I'll also make plans for adding proper support for single-end reads. We can use this issue to track progress on that.

[Rubbert]

Hi @aryarm ,

Perfect, I'll see if I can give that a go, and let you know if I run into any issues.
I'd already started writing the scripts for SNP calling with GATK (chosen based on your paper), and I can hopefully compare the results. Additionally, when I get the full set of data, I should also have data from a SNP-array, which I could use to check the consistency with the SNPs common to ATAC-calling and the SNP-array.

Cheers!