Convert a VCF-file in a user specific Format

Convert a VCF-file in a user specific Format

0

Hello everyone,

I am curious if it is possible to convert a VCF-File (with multiple samples) in a Format whith 5 columns.

  1. Column should be Sample ID
  2. Column: Position on the chromosome
  3. Genotyp
  4. Number of reads covering site
  5. QUAL phred-scaled quality score for the assertion made in ALT.

May there is allready a tool which can perform this, or if I need to do it myself may you can recommend me a good programm (like awk or sed) and recommend me a code.

Aim of this should be that afterwards i can filter variants via Quality score and number of reads covering site.

Thanks a lot in advance


VCF

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