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  • multiple vcf files to one multisampled vcf file

    Hello everyone,

    Does anyone know how I can create one multisampled vcf file of multiple vcf files? Now I have many vcf files which all contain the SNPs of one sample.

    Does the program bcftools cat create a multisampled bcf file, or does this one only combine the bcf files?

    Or do I have to use samtools mpileup again, now with multiple samples in once?

  • #2
    Try with vcftools vcfmerge (or the improved htscmd)



    However, if you want a complete sample-specific information on all variant positions, you'll need to re-run mpileup again

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    • #3
      Thanks!
      This program looks like it does exactly what I want!

      [EDIT]
      I used this program for combining the vcf files, but the output is not good enough.
      We are going to rerun the samtools mpileup, exactly because the reason you mentioned: the sample-specific information on all variant positions
      Last edited by Jetse; 06-28-2013, 03:26 AM. Reason: new insights

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