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  • vcfTools depth filter problem

    Hey guys,

    I am new to vcf and having difficulty filtering my SNPs in vcfTools.

    I have a vcf file (fileformat=VCFv4.1) of SNPs found in a group of individuals of a species (pooled as one individual for the time being).


    sample:
    Spp1_cDNA-30 211 . G A 122 . DP=15;VDB=0.0017;AF1=1;AC1=2;DP4=0,0,0,12;MQ=60;FQ=-63 PL 155,36,0

    I want to apply some simple filters e.g. depth.

    However the output file generated gives me depths of 0 at all SNPs despite the vcf giving sensible DP values.

    Similarly, mean depth stat calculation returns 0 for the entire vcf.

    What am I doing wrong here guys?

    Any help will be much appreciated.

    Thanks,

    J

  • #2
    Can you post the command you ran? Based on the one line of VCF you've posted, there seem to be 12 reverse reads with non-ref allele. You can filter your input using the DP4 field.

    Description of DP4 from http://samtools.sourceforge.net/mpileup.shtml
    "DP4: Number of 1) forward ref alleles; 2) reverse ref; 3) forward non-ref; 4) reverse non-ref alleles, used in variant calling. Sum can be smaller than DP because low-quality bases are not counted."

    Comment


    • #3
      OK thanks for pointing that out.
      However, Im not sure the significance of what that actually means?
      "12 reverse reads" is fine as far as I figure.
      And overall depth is 15 (including low quality bases I presume?)

      Here is my command:

      vcftools --vcf file1.vcf --minDP

      Testing some other functions, vcftools wont actually calulate any for me.

      Eg.

      vcftools --vcf SkateGenotypes.vcf --counts

      I have attached a sample of my vcf file.

      Thanks alot!
      J

      CHROM POS N_ALLELES N_CHR {ALLELE:COUNT}
      Skate_cDNA-0 48 2 0 G:0 A:0
      Skate_cDNA-0 49 2 0 G:0 A:0
      Skate_cDNA-0 176 2 0 A:0 G:0


      Addtional:

      When I run vcf-stats on the compressed file I get the following error:

      Use of qw(...) as parentheses is deprecated at /usr/share/perl5/VcfStats.pm line 428.
      Use of qw(...) as parentheses is deprecated at /usr/share/perl5/VcfStats.pm line 433.
      Could not parse the fileformat version string [VCFIDX], assuming VCFv4.1
      Broken VCF header, no column names?
      at /usr/share/perl5/Vcf.pm line 171, <$__ANONIO__> line 1.
      Vcf::throw('VcfStats=HASH(0x1549010)', 'Broken VCF header, no column names?') called at /usr/share/perl5/Vcf.pm line 845
      VcfReader::_read_column_names('VcfStats=HASH(0x1549010)') called at /usr/share/perl5/Vcf.pm line 589
      VcfReader:arse_header('VcfStats=HASH(0x1549010)') called at /usr/share/perl5/VcfStats.pm line 53
      VcfStats:arse_header('VcfStats=HASH(0x1549010)') called at /usr/bin/vcf-stats line 137
      main::vcf_stats('HASH(0x11ac480)') called at /usr/bin/vcf-stats line 12
      Attached Files
      Last edited by JackieBadger; 08-13-2013, 09:50 AM.

      Comment


      • #4
        No one has any insight here?

        Could it be that the chromosome names (which are actually reference coltigs) are stings that do not include < > ?

        Should I just remove the wording, to have just numbered chromosome IDs?

        If so whats the best way to do this?

        I did it in excel and with the following perl script but it then leave the output.vcf unreadable by vcftools:

        perl -pe 's/^Little_Skate_cDNA-//' SkateGenotypes.vcf > SkateGenotypesError.vcf

        Any help would be greatly appreciated.

        Cheers,

        J

        Comment

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