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  • suryat
    replied
    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.

    Leave a comment:


  • plreddy
    replied
    Great tool for splitting vcf files

    Leave a comment:


  • Brian Bushnell
    replied
    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.

    Leave a comment:


  • htetre
    replied
    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

    Leave a comment:


  • rajeshkmaurya08
    replied
    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?

    Leave a comment:


  • SNPsaurus
    replied
    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

    Leave a comment:


  • rajeshkmaurya08
    replied
    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?

    Leave a comment:


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

    Leave a comment:


  • willMD
    started a topic extract a chromosome with vcftools

    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!

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