Greetings,

what is the difference between the prebuilt HISAT2 indexes grch38.tar.gz and grch38_snp.tar.gz found here? The readme file is not very clear, at least to 40 IQ me:

HISAT2 indexes named genome_tran or genome_snp_tran use Ensembl gene annotations, which include many more transcripts than RefSeq annotations, due to the inclusion of annotations as predicted by software

If I am trying to align tumour and matched normal exome data for subsequent variant calling, which one should I be using, and how would my output be different?

Thanks in advance.