working with hg38

[rajithadp]

I'm trying to analyze my nanopore data, generated using the hg38 reference sequence. Can you please include instructions on how to run infoGenomeR with the hg38 setup? As far as I understand, it runs with hg19 by default.

[yhunlee]

I'm working on the hg38 automation. Just need to include bwa indices and mappability files.

For nanopore data, I haven't run it standalone.
The way that I have been used long reads is,

1. Start from a short-read fastq/bam. CNA/SNP/SVs are called based on it.
2. Feed nanopore SV calls into the pipeline, additionally (--additional-sv option should be introduced soon).