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Thread: How extract ChrMt 16Kb fasta from BAM.Which metrics (Kulczynski,Hamming,Jaccard,Kamur

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    How extract ChrMt 16Kb fasta from BAM.Which metrics (Kulczynski,Hamming,Jaccard,Kamur

    Question about ChrMt 16Kb fasta file: any idea of online tools or Windows tools for converting/extracting such a fasta file from BAM file generated by Dante Labs WGS 30x test?
    I have tried BAM Analysis Kit 1.8 but it produced a VCF file, not fasta. With remark that some reads might be filtered, which leaves room for questioning wheather it is 100% of the ChrMt. Further I found an online tool, which accepted vcf format for ChrMt analysis (https://haplogrep.uibk.ac.at/).

    It is very informative and applies for different MtDNA metrics (Kulczynski, Hamming, Jaccard, Kimura2P). Now, it returned three main options for MT Haplogroup assignment ([J2a1a1a], [H2a2a1], [H85]). Here is my essential question: is it normal or could be something to do with the initial (questionable) vcf file, or not.

    And again the technical quaetsion: is there a way I could extract ChrMt 16Kb fasta file from a BAM (WGS) directly?
    Last edited by Tonev; 03-23-2019 at 04:19 PM.

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