Which GrCh38 reference file to use ?

[Krithika-Bhuvan]

Your documentation says to use "hg38 reference without alt contigs". Could you provide a link to which reference genome file you used ? I would like to try the same reference genome file. Thanks.

[jfass]

I used GENCODE's GRCh38 primary assembly fasta file, without an obvious problem:

ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_31/GRCh38.primary_assembly.genome.fa.gz