Question: about filtering variants from a VCF file
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2.9 years ago by
Bogdan580
Palo Alto, CA, USA
Bogdan580 wrote:

Dear all,

for filtering a VCF file based on various criteria (Allelic Depth or Allelic Frequency, etc), which libraries would in BioC you recommend to use ? thank you ;) !

-- bogdan

vcf • 612 views
modified 2.9 years ago • written 2.9 years ago by Bogdan580
1
2.9 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

VariantAnnotation::filterVcf() (and vignette) would be one candidate; TVTB also implements filters, with an extensive vignetteHelloRanges translates bedtools queries to GRanges functions, which can be used on VCF objects from VariantAnnotation.

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2.9 years ago by
Bogdan580
Palo Alto, CA, USA
Bogdan580 wrote:

Dear Martin, thank you and happy and fruitful new year ! yes, I have started with VariantAnnotation(); and I may have some little questions along the way ;) thanks for your help !

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2.9 years ago by
Bogdan580
Palo Alto, CA, USA
Bogdan580 wrote:

Hi Martin, please when you have a minute, may I ask you for a suggestion : shall I have a VCF file as it is described below, what would be the fastest way to select only the variants with AD > 5, and AF > 0.05 ? thanks !