[Question]: difference between sites.hg38.vcf.gz and sites.hg38.rna.vcf.gz

[tamuanand]

Hi @brentp

I had a question on the difference between sites.hg38.vcf.gz and sites.hg38.rna.vcf.gz and when to use one or the other

• #75 (comment)

are you using this sites file: https://github.com/brentp/somalier/files/4566475/sites.hg38.rna.vcf.gz
for RNA-seq? I should probably make that the default for WGS as well.

• #79 (comment)

You must run somalier extract with the same sites for all samples and assays. I recommned to use sites.hg38.rna.vcf.gz that will work well for WGS too.

Is sites.hg38.rna.vcf.gz supposed to be for RNASeq and WGS? Likewise is sites.hg38.vcf.gz supposed to be for WES?

Thanks in advance.

[Brent Pedersen]

Hi, if you have any samples with RNA, seq, I would use sites.hg38.rna.vcf.gz. Otherwise, use sites.hg38.vcf.gz (which will work for WES).
I expect both should give very similar results on WES/WGS, but the sites.hg38.rna.vcf.gz will likely have more usable sites on RNA-Seq.

[tamuanand]

Thanks @brentp