Question: VariantAnnotation package, subseting vcfs on fixed fields
0
gravatar for Anna N.
4.9 years ago by
Anna N. 0
France
Anna N. 0 wrote:

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

ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by Anna N. 0
Answer: VariantAnnotation package, subseting vcfs on fixed fields
3
gravatar for Valerie Obenchain
4.9 years ago by
United States
Valerie Obenchain6.7k wrote:

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

ADD COMMENTlink written 4.9 years ago by Valerie Obenchain6.7k
Answer: VariantAnnotation package, subseting vcfs on fixed fields
0
gravatar for Anna N.
4.9 years ago by
Anna N. 0
France
Anna N. 0 wrote:

much obliged!

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

Anna

ADD COMMENTlink written 4.9 years ago by Anna N. 0
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