Question: Find SNPs in the exome from WGS data
0
gravatar for jh
19 months ago by
jh10
jh10 wrote:

Hello,

I have called variants in WGS data with GATK. Now I would like to filter out alla heterozygous SNPs in the exome and which genes they are present in.

The output should be structured:

chrom | position | GT (nucleotides) | gene

1 | 100 | A/T | geneA

1 | 200 | G/T | geneA

2 | 100 | A/C | geneB

Thanks for any help!

joanna

sequencing snp gene • 561 views
ADD COMMENTlink modified 19 months ago • written 19 months ago by jh10

Thanks a lot for the advice, VEP works great!

I can't figure out how to print the reference allele as a separate column.

Does anyone know?

Best

ADD REPLYlink written 19 months ago by jh10
7
gravatar for andrew.j.skelton73
19 months ago by
Newcastle Upon Tyne
andrew.j.skelton734.2k wrote:

You could use Ensembl's VEP to annotate all your filtered variants, then filter based off that. Alternatively, you could try Gemini, which would allow you to make complex and flexible queries around large sets of data (based on SQLite)

ADD COMMENTlink written 19 months ago by andrew.j.skelton734.2k

I would highly recommend GEMINI (which you can use on VEP or SnpEff annotated VCF files). It will let you do family-wise queries and lots of different ways of slicing the data. But even for the simple case you describe I think you'll likely find all of the additional capabilities appealing.

ADD REPLYlink written 19 months ago by Dan Gaston6.9k
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