I tried to make new HISAT2 index for the maize version 4 genome including SNP informations. However, I had multiple issues while doing it. After an hour work, finally get it done.

Change variable names and more

In the make_zm4_snp_tran_ercc.sh file which provided by the HISAT2 team in their FTP server, multiple variables are indicated at first. It really helps to reduce changes. But, there are also several places that need to change manually.

For example:

GTF_FILE=Zea_mays.AGPv4.37.gtf
F=Zea_mays.AGPv4.dna.toplevel.fa

Use python 2!

One of the problem is those helper python scripts provided by the software are in Python 2 (which I did not find any documentation indicating this). The default python version on our server is Python 3.6, so the hisat2_extract_snps_haplotypes_VCF.py wont’t work. It report the following errors:

TypeError: startswith first arg must be bytes or a tuple of bytes, not str

Luckily, the fix is easy. Just change the first line of that script to (or where your python 2 is):

#!/usr/bin/python2.7

Then it works great.

It tooks 03:43:45 for building index.