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How to annotate my genome with clinker using BCFTools

Hi all,

I have my WGS in VCF format from nebula genomics. I've changes the chromosome notation to match clinker VCF file, normalized, decomposes and reindexed.

I successfully ran the following BCFTools command on it and the clinker VCF

bcftools annotate -a /clinvar.vcf.gz -c =ID,INFO myvcf.gz | bgzip > test2.vcf.gz

and was able to use a text editor to find all the variations I have that are in clinker

However I would prefer two differences in the output

  1. the output file should contain only the matching rows (matching between clinker and my vcf). the current output has every row in my vcf, it just adds the ID and INFO fields from clinker to the matching rows.
  2. i would prefer that the INFO from clinker be appended or added a new column, rather than overwriting the INFO in my vcf.

Is this possible? How would I do it?

bcftools clinvar
• 1,300 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Seth • Seth

better:

bcftools annotate -a /clinvar.vcf.gz -c =ID,INFO  -O z -o  test2.vcf.gz myvcf.gz
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

1 answer

the output file should contain only the matching rows i would prefer that the INFO from clinker be appended or added a new column, rather than overwriting the INFO in my vcf.

Could be something like, don't put the whole INFO tag in annotate:

bcftools annotate -a /clinvar.vcf.gz -c 'ID,INFO/AF_ESP,INFO/RS'  -O u  myvcf.gz |\
bctools view -i 'INFO/RS!=""'   -O z -o  test2.vcf.gz
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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