Question

I am trying to use SED command to replace/remove rs numbers from my file.
I have a VCF file:

##reference=file:/hs37d5.fasta

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  SC_PCHD5235298

1       10234   rs145599635     C       T       153.34  .

I would like to replace rs* entries ONLY on the lines which does not start with #,
For example i would like to replace rs145599635 with a dot. And want it to ignore headers which are the lines start with a #.

I tried

sed "/^[^#]/s/rs.*/./g" test.vcf

but it deletes everything after the rs.

Answer 1

You can try with this,

Ex:

  sed -i 's/\(^[^#].*\)rs[0-9]\+\( .*\)/\1rs.\2/' test.vcf

I altered your command.You have to write like this.

   sed -i "/^[^#]/s/rs[0-9]\+/rs./g" test.vcf

My test.vcf file looks like this.I think your file looks like this only.

  ##reference=file:/hs37d5.fasta

  #rs145599635 C T 153.34 .
  #1 10234  rs145599635 C T 153.34  .
  #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SC_PCHD5235298

  1 10234  rs145599635 C T 153.34  .

I hope this will help you.