exceeded integer bounds, remove adjacent SNPs, use haplotypes, or switch to a large index (--large-index)

DaehwanKimLab / hisat2

Graph-based alignment (Hierarchical Graph FM index)

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exceeded integer bounds, remove adjacent SNPs, use haplotypes, or switch to a large index (--large-index) #289

Open shanwai1234 opened 3 years ago

shanwai1234 commented 3 years ago

Hello, I am using Hisat2 to build genome index with SNP. I have ~7 millons of SNPs and my genome size is around ~2G. But it always report me this error when I built genome index with --snp. Is there any limitation for the SNP number? since I have reduced my SNP number from ~10 millions to ~7 millions, do you have a concept how many numbers of SNP would work under this circumstance? Thank you!

yjiang296 commented 1 year ago

Hello, I met the same circumstances. I wonder whether you have fixed this problem. Could you give me some advices?

shanwai1234 commented 1 year ago

What I did was to switch to the "N-masked" approach. First you will need to replace SNP by N in your genome and then using SNPsplit to generate allele-specific counts from your bam file output.