hisat2-build --snp build personal index but mapping result doesn't change
I used this command to build hisat2 index :
hisat2-build -p 16 ~/hg19/chr19.fa --snp snps.txt genome ;
the snps.txt only has 300 SNPs ;
I used this index and hisat2 index built without snps to map, but the results (bam file) are the same... But when I used this individual's all SNPs (about 370w) to build index, the result is different... I don't know if it is caused by too few SNPs to build... Could someone give me some advice?
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