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  • Convert VCF files to BCF files

    I know this question might sound stupid but is there any way we could convert vcf files to bcf files?

    I created vcf files to each genome and then concatenate them to create the vcf files. I want to know is there anyways to convert it to a bcf file?

  • #2
    Convert VCF files to BCF files

    First off, you need to have a file with all of the chromosome identifiers. So, if you have 3 chromosomes labeled A01, A02, and A03, you need a file with this list:
    A01
    A02
    A03
    Then you run the following command (with the appropriate file names):
    bcftools view -Sb -D chromosome.txt file.vcf > file.bcf

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    • #3
      can you tell me how to create a index of vcf file other than IGV

      Comment


      • #4
        Originally posted by Momina View Post
        can you tell me how to create a index of vcf file other than IGV
        For all those people who find it more convenient to bother you with their question rather than to Google it for themselves.

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