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  • extract a chromosome with vcftools

    I tried to extract Chr 1 data and recode a new vcf using the example in the basic documentation and got no data out. All I want to do is break the large input file into small files of one chromosome each.

    this is the log file:

    VCFtools - v0.1.10
    (C) Adam Auton 2009

    Parameters as interpreted:
    --gzvcf /Users/williamcassano/Desktop/Variations/PG0000652-BLD.genome.block.anno.vcf.gz
    --chr 1
    --out chr1
    --recode

    Using zlib version: 1.2.5
    Reading Index file.
    File contains 128054613 entries and 1 individuals.
    Filtering by chromosome.
    Chromosome: chr18
    Chromosome: chr3
    Chromosome: chr20
    Chromosome: chr17
    Chromosome: chr8
    Chromosome: chr19
    Chromosome: chr15
    Chromosome: chr10
    Chromosome: chr12
    Chromosome: chr16
    Chromosome: chrX
    Chromosome: chr14
    Chromosome: chr5
    Chromosome: chr22
    Chromosome: chr2
    Chromosome: chr6
    Chromosome: chr7
    Chromosome: chr1
    Chromosome: chr9
    Chromosome: chr13
    Chromosome: chr21
    Chromosome: chrM
    Chromosome: chrY
    Chromosome: chr4
    Chromosome: chr11
    Keeping 0 entries on specified chromosomes.
    Applying Required Filters.
    After filtering, kept 1 out of 1 Individuals
    After filtering, kept 0 out of a possible 0 Sites
    Error:No data left for analysis!

  • #2
    You may have to put '--chr chr1' instead of '--chr 1'. Your vcf file has chromosoms marked as 'chr$number'.
    Good luck

    Comment


    • #3
      i have applied this vcftools but it showing following program
      My input command :
      vcftools --gzvcf ExAC.r0.3.1.sites.vep.vcf.gz --chr chr21 --out chr21 --recode

      And error is showing like this:

      VCFtools - UNKNOWN
      (C) Adam Auton and Anthony Marcketta 2009

      Parameters as interpreted:
      --gzvcf ExAC.r0.3.1.sites.vep.vcf.gz
      --chr chr21
      --out chr21
      --recode

      Using zlib version: 1.2.8
      After filtering, kept 0 out of 0 Individuals
      Outputting VCF file...
      After filtering, kept 0 out of a possible 0 Sites
      File does not contain any sites
      Run Time = 0.00 seconds

      I am getting all these things as log file as output?

      Could anyone please help me to split the chromosome21.vcf from my input file with proper command line discription?

      I have looked and tried all vcf command and and even gatk too?

      Comment


      • #4
        I think you have the opposite problem as the original poster. They used --chr 1 but the vcf used chr1 instead of 1 to describe the chromosome number. You are using --chr chr21 but it looks like ExAC uses 21 instead of chr21 to describe the chromosome number.
        #CHROM POS ID REF ALT QUAL FILTER INFO
        1 13372 . G C 608.91 PASS
        Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

        Comment


        • #5
          yes you right,
          but vcf tool was not giving output.

          so i tried with tabix

          tabix -h file_name 21

          it vcf file of chr 21 but i am not sure about its ending statement.

          is it right to extract by this command?

          Comment


          • #6
            Keep all chromosomes and remove scaffolds

            Hello,

            I am trying to do something similar, I want to keep information for 10 chromosomes (Chr01-10) and remove the scaffold SNP information in my vcf file.

            This is the code I have run
            vcftools --vcf original.vcf --out varCHR.vcf --chr Chr[01-10]

            And I receive the following
            After filtering, kept 2 out of 2 Individuals
            After filtering, kept 0 out of a possible 166402 Sites
            No data left for analysis!
            Run Time = 0.00 seconds

            Can anyone help me with my problem?
            Thank you

            Comment


            • #7
              You can also use BBMap's filtervcf.sh like this:

              Code:
              filtervcf.sh in=original.vcf out=varCHR.vcf contigs=Chr01,Chr02,Chr03,Chr04,Chr05,Chr06,Chr07,Chr08,Chr09,Chr10
              ...assuming those chromosome names are correct. Please let me know if that does not work.

              Comment


              • #8
                Great tool for splitting vcf files

                Comment


                • #9
                  vcftools can do this, here is a command
                  vcftools --chr chr1 --vcf myfile.vcf --recode --recode -INFO-all --out myfile.chr1.vcf

                  check your vcf file first to assure how chromosome number has been marked. (chr1 or 1) use that in command line.

                  Comment

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