Aldy can not create profile for hg38
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When I use the following command:
aldy profile --cn-neutral-region chr22:17400001-21700000 my.bam > my.profile
I get the profile and when I use it in:
aldy genotype -p my.profile -g cyp2d6 my.bam --param sam_long_reads=true
I get this error:
🐿 Aldy v4.5 (Python 3.8.10 on Linux 5.15.0-105-generic-x86_64-with-glibc2.29)
(c) 2016-2024 Aldy Authors. All rights reserved.
Free for non-commercial/academic use only.
Genotyping sample my.bam...
ERROR: gene= cyp2d6, profile= my.profile, file= my.bam
Profile my.profile not compatible with hg38
my.bam is ONT data and it's indeed aligned with hg38!
While Aldy seems does not create a profile for hg38 bam file, surprisingly it will works perfectly in creating a profile file from hg37 bam file! Here the only problem is the tool not work with hg37 and I get this error:
ERROR: gene= cyp2d6, file= myhg37.bam
AssertionError('Only hg38 supported at this moment')
Apparently, Aldy in the latest documentation accepts ONT data where it says:
Note: if you are using long-read captures such as PacBio or Nanopore, make sure to add the following lines to the corresponding profile file:
options:
sam_long_reads: true
Alternatively, you can pass this flag directly to Aldy as --param sam_long_reads=true.
Alright. Making profile for hg38 is done now through following command:
aldy profile --genome hg38 My.bam > MyProfile.profile
Just in case if somebaody faced similar problem.