Question of setting the -H parameter
vegetableyu opened this issue · comments
Hi there,
I would like to kindly inquire, if I input a BAM file that is aligned to 'GRCh38_full_analysis_set_plus_decoy_hla.fa', when executing 'ERVcaller_v1.4.pl', should the '-H' parameter input be 'GRCh38_full_analysis_set_plus_decoy_hla.fa', or should it still be the 'hg38.fa' without ALT contig?
I appreciate your guidance on this matter. Thank you.
Hi,
It would say that it would be better to use the same reference genome as the input BAMs even though it may not change the results.
Best,
Xun