Hello

I have a large vcf file and I would like to keep only the pass entries in the filter column.

Is there a way to do this with Variant Annotation?

I know that we can subset on the fields
eg

## Subset on 'fixed', 'info' or 'geno' fields:
  param <- ScanVcfParam(fixed="ALT", geno=c("GT", "HQ"), info=c("NS", "AF"))
  vcf_tab <- readVcf(tab, "hg19", param)

but can we further select entries within these fields?

Thank you in advance
Anna

Hi Anna,

You can filter on field values with filterVcf(). This function outputs another VCF file which you can then read in with readVcf().

Examples of how to construct the filters are on the man page,

?filterVcf

and in the 'filterVcf Overview' vignette,

browseVignettes("VariantAnnotation").

Valerie

much obliged!

I can filter my vcfs using other tools, but I would prefer to have a full pipeline using VariantAnnotation.
 

Anna