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  • Extract reference and aligned sequences from BAM file basing on VCF file

    I couldn't find relevant information. I hope it's not duplicate.

    I have resequencing data for two maize lines (BAM and VCF files).
    I want to extract sequences (fasta) for several genes (I have also GFF3 file with annotation data) from reference genome and corresponding sequences from resequencing data. I probably could use sequence identifiers, as they are in my files

    Which tool allows to extract such data, and more generally to extract sequences for
    a given variant type (SNP, indel, etc) and location (exon, intron, etc)?
    Last edited by floem7; 01-17-2015, 03:24 PM. Reason: Adding info.

  • #2
    You can try

    - "vcf-consensus" from VCFtools: http://vcftools.sourceforge.net/perl...#vcf-consensus. Click on "Read more" to get an example how to get the consensus for a given region within the reference sequence (you need to extract this information from your GFF).

    or

    - FastaAlternateReferenceMaker within GATK (https://www.broadinstitute.org/gatk/...renceMaker.php)

    Read the documentation thoroughly - there are several caveats!

    Comment


    • #3
      Forgot to mention, if you just want to extract FASTA sequences for GFF features (i.e. without any called variants applied), you can use BEDTools getfasta (http://bedtools.readthedocs.org/en/l.../getfasta.html).

      Comment


      • #4
        Thanks, I've followed example found at vcftools page and it works :-)

        Great thanks!

        Edit: however, I realized that aligned fasta format would be better. The aim is to quickly generate
        friendly msa view for a given region. For example for primer design.

        Certainly, ordinary MSA programs don't create sufficiently similar alignment as this in bam file.
        So it require manual inspection.
        Last edited by floem7; 01-19-2015, 02:45 PM. Reason: adding info.

        Comment

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