Question: Querying variations from a VCF file
0
gravatar for Arko
6 months ago by
Arko10
US/Boston/Boston University
Arko10 wrote:

I have a VCF file v4.1 and I'm trying to extract the type of variations (Substitution, Insertion, Silent, Intergenic, etc.) from it. If there are multiple possibilities, how would I annotate the most deleterious possibility? Apart from that, I'm trying to find the number of reads supporting the variant and the percentage of reads supporting the variant versus those supporting reference reads.

Can anyone elaborate on how to go about this? Thanks in advance!

ADD COMMENTlink modified 6 months ago by Emily_Ensembl18k • written 6 months ago by Arko10

d I'm trying to extract the type of variations (Substitution, Insertion, Silent, Intergenic, etc.)

see the questions about VEP/SnpeFF...

I'm trying to find the number of reads supporting the variant and the percentage of reads supporting the variant versus those supporting reference reads.

see the VCF specification about FORMAT/AD.

ADD REPLYlink written 6 months ago by Pierre Lindenbaum119k
1
gravatar for Emily_Ensembl
6 months ago by
Emily_Ensembl18k
EMBL-EBI
Emily_Ensembl18k wrote:

This table is the ranking order Ensembl and the VEP use.

ADD COMMENTlink written 6 months ago by Emily_Ensembl18k
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