[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

• https://github.com/brentp/somalier/issues/75#issuecomment-852399046

  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.

• https://github.com/brentp/somalier/issues/79#issuecomment-883937825

  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.

[brentp]

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