We encountered an issue where the output files (.snp and .haplotype) generated by the hisat2_extract_snps_haplotypes_UCSC.py and hisat2_extract_snps_haplotypes_VCF.py commands were empty, despite following the provided instructions and using the updated SNP database file (snp151Common.txt). We are currently investigating the cause of this problem and working on finding a solution.
We encountered an issue where the output files (.snp and .haplotype) generated by the hisat2_extract_snps_haplotypes_UCSC.py and hisat2_extract_snps_haplotypes_VCF.py commands were empty, despite following the provided instructions and using the updated SNP database file (snp151Common.txt). We are currently investigating the cause of this problem and working on finding a solution.