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  • cowman
    Member
    • Jan 2011
    • 14

    #1

    Problem converting bcf to vcf

    The bcf tools manual says that the default output is vcf so I expected the following command to produce a vcf file:

    bcftools view 0000.bcf > chr10.vcf

    The file 0000.bcf is 24M in size and the file chr10.vcf is 1.9G in size so something has clearly happened but opening chr10.vcf shows it is still binary (see below).

    0000.bcf was generated with the htslib version of vcf isec

    Any suggestions where I am going wrong?

    Thanks

    ##fileformat=VCFv4.1
    ^@^@^@<A7>^A^@^@^@^@^@^@<95>{<A9>^@^A^@^@^@{<B4><B3>C^O^@^B^@"^@^@^E^G^WG^WA^@^Q^F^Q^B^Q^G^U<98>n^R>^Q^H^Q^N^Q ^U^<BA> ?^Q^B^Q0^Q^K^U^@^@^@^@^Q^L^U^Y^D<A6>?^Q^M^U@^S<A1>>^Q^O^Q^B^Q^P^U<98>n^R>^Q^Q^U33%B^Q^R^Q^H^Q^S^U^<BA><99>?^Q^T^U<B8>^^]A^Q^W^U<DB><F9>^^?^Q^D!^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^B^B^@^@^@^@^@^@^B^B^@^@^B^B^B^B^@^@^@^@^@^@^@^@^B^B^@^@^@^@^@^@^@^@^@^@^@^@
    ^@^@^@^@^@^@^B^D^B^D^Q^A!<80><80><80><80><80><80><80><80><80><80><80><80><80><80><80><80><80><80><80><80>^E^@<80><80><80><80><80><80>^E^@<80><80>^A^@^B^@<80><80><80><80><80><80><80><80>^B^@
    <80><80><80><80><80><80><80><80><80><80><80><80><80><80><80><80><80><80>^H^O^B^A^Q^B^Q<80><80><80><80><80><80><80><80><80><80>^E<80><80><80>^E<80>^A^B<80><80><80><80>^B<80><80><80><80><80>
    <80><80><80><80>^V^C^Q^C^Q<80><80><80><80><80><80><80><80><80><80>^O<80><80><80> <80>^C^C<80><80><80><80>^F<80><80><80><80><80><80><80><80><80>c^U^Q^E2^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@<80>^@^@^O^@<95>^@^@<80>^@<80>^@<80>^@<80>^@<80>^@

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