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  • Error using vcf-stats

    I am trying to figure out the variant statistics from a vcf file using the command:
    Code:
     ./vcf-stats NA11881roi_variants.vcf
    For which I am getting the following output:

    Code:
    The version "4.1" not supported, assuming VCFv4.0
    Expected GT as the first genotype field at chr4:46036725
    Use of uninitialized value $gtype in pattern match (m//) at /N/dc/scratch/bansalr/bowtie2-2.1.0/vcftools_0.1.4a/perl/Vcf.pm line 1060, <__ANONIO__> line 28.
    Use of uninitialized value $gtype in concatenation (.) or string at /N/dc/scratch/bansalr/bowtie2-2.1.0/vcftools_0.1.4a/perl/Vcf.pm line 1060, <__ANONIO__> line 28.
    Could not parse gtype string []
    
     at /N/dc/scratch/bansalr/bowtie2-2.1.0/vcftools_0.1.4a/perl/Vcf.pm line 167, <__ANONIO__> line 28.
            Vcf::throw('Vcf4_0=HASH(0x260f630)', 'Could not parse gtype string []\x{a}') called at /N/dc/scratch/bansalr/bowtie2-2.1.0/vcftools_0.1.4a/perl/Vcf.pm line 1060
            VcfReader::parse_alleles('Vcf4_0=HASH(0x260f630)', 'HASH(0x25221d8)', 'NA11881roi.sorted.bam') called at ./vcf-stats line 83
            main::vcf_stats('HASH(0x2237de8)') called at ./vcf-stats line 9
    Can somebody please help me regarding this? I am new to this field

    Thank you!

  • #2
    It looks like the vcftools you are using is of version 0.1.4a. So the first thing i would try is to install the updated version, which is 0.1.11.

    Comment


    • #3
      VCFtools error

      Originally posted by yl01 View Post
      It looks like the vcftools you are using is of version 0.1.4a. So the first thing i would try is to install the updated version, which is 0.1.11.
      Hi, I have same error when I run vcf-isec even I installed the updated version.

      Use of uninitialized value $attr_value in pattern match (m//) at /home/../vcftools_0.1.11/perl/Vcf.pm line 2971, <__ANONIO__> line 6.
      at /home/bliu1/vcftools_0.1.11/perl/Vcf.pm line 2971.

      Could you help? thanks

      Comment


      • #4
        I've just started using bcftools stats, so I still don't know much, but for me, I get an error when I don't give a bgzip compressed file, could that be your case? You can get the bgzip in the htslib package, after that, you need to index the bgzip file with bcftools index. Do you think that would help?

        By the way, just getting a ride on your question, does anyone know where to find the documentation for the bcftools stats output? I've got some weird results that I would like to understand better. I've asked the same question here: http://seqanswers.com/forums/showthread.php?t=57687

        Comment

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