Question: Targeted capture sequencing data
0
gravatar for MAPK
4.8 years ago by
MAPK1.7k
MAPK1.7k wrote:

I am working on whole genome and exome genotyping data and also need to do some analysis with the targeted genotyping data. Is there any database I can go to download these targeted capture data sets ? I have tried Illumina website, but all they have is information on targeted capture method and don't have any output data (sample data) from targeted capture.

targeted sequencing • 1.4k views
ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by MAPK1.7k
1
gravatar for rbagnall
4.8 years ago by
rbagnall1.7k
Australia
rbagnall1.7k wrote:

Do you mean you want to download fastq data from Illumina exome enrichments, and from Illumina targeted sequencing, such as the TruSight capture panels?

If you register for a BaseSpace account than you can access an assortment of different datasets:

BaseSpace Public datasets

If you want the resulting genotypes (in vcf format?) then I'm not sure.

ADD COMMENTlink written 4.8 years ago by rbagnall1.7k

I need the resultant genotypes in vcf format. Thanks

ADD REPLYlink written 4.8 years ago by MAPK1.7k

Then you can run them through BaseSpace analysis pipelines.

ADD REPLYlink written 4.8 years ago by igor12k

@Igor Thanks, Do you know exactly which pipeline I can run in this case?

ADD REPLYlink written 4.8 years ago by MAPK1.7k
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