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  • Viewing vcf and bam files in artemis

    Dear All, I'm new to Artemis and could do with some help viewing vcf files.

    1) First I loaded my embl reference file
    2) Then I index my vcf files with tabix as per the manual
    3) Then I go to File > Read BAM/VCF
    4) Find the file and select it (but nothing seems to happen in the viewer)

    When I click on Display > VCF also nothing happens

    I've even tried using bcftools to index the bcf files and upload them but that doesn't work either.

    What am I doing wrong? I should be able to load various vcf files?

    I'd be really grateful for some guidance on this. Many thanks.

  • #2
    problem with vcf file reading on artemis

    I got the same problem..still trying to fix it up

    Comment


    • #3
      you need to zip your VCF file first and then index
      bgzip file.vcf
      tabix file.vcf.gz

      Comment


      • #4
        Hi there, I am having a similar problem with my BAM files.

        I have some transcriptome data in BAM format (alongside the BAM sorted and sorted.bai index files made with SAM tools).

        When i read the BAM file nothing happens on my screen.

        Thanks

        Comment

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