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How to generate VCF from HISAT2 pre-built SNP index?

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  • How to generate VCF from HISAT2 pre-built SNP index?

    My ultimate goal is to get a (n= samples, m= SNPs) data matrix. My plan was to use HISAT2 for the mapping, VCF tools for the vcf file, and then parse it to generate the data matrix I can actually mine.

    I'm using the pre-built SNP index file for H. sapiens, Ensembl GRCh38 . I have HISAT2 running smoothly for all of my samples and started reading the downstream pipeline for generating VCF files (

    samtools mpileup -uf $HISAT2_HOME/example/reference/22_20-21M.fa eg2.sorted.bam | bcftools view -bvcg - > eg2.raw.bcf
    How do I get the original fasta file or build a VCF file using this index and my sam/bam files? I was going to just download the hg38 Ensemble annotated genome but I don't think that's what I need. . . I went into the ``file from the tar ball when downloading the SNPs db. I think it's building the SNP index from `Homo_sapiens.GRCh38.dna.primary_assembly.fa. Is this the file that needs to be used? (

    Also, if anyone has any insight on how to generate a data matrix from the vcf files, it would be greatly appreciated (but first I need to generate the vcf files)

    Thanks in advance
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    Last edited by jol.espinoz; 04-30-2017, 11:26 AM.