You can use Cohort browser to select participants based on their EIDs and then use Variant browser to search for particular rsID. This will work if you have access to 450K WES. If not, you can use bcftools to filter VCF file as following:
Yes, if you put the SNP in a basket, you can download it as part of the main tabular dataset for that basket, and there will be one EID per row and one value of the SNP per row.
The SNP will be listed in the dataset by the AffyID.
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You can use Cohort browser to select participants based on their EIDs and then use Variant browser to search for particular rsID. This will work if you have access to 450K WES. If not, you can use bcftools to filter VCF file as following:
bcftools view -s 1234567, 1234568 --include ID==@snps.list vcf_file.vcf
snps.list contains 1 rsID per line
rs575563330
rs572898889
rs141149254
Here is discussion on how to filter VCF file by rsID on biostars.
Thank you Anastazie!!!!
Hi! is it possible to know which rsID matches the specific EID? (which means EID and rsID in a row).
Yes, if you put the SNP in a basket, you can download it as part of the main tabular dataset for that basket, and there will be one EID per row and one value of the SNP per row.
The SNP will be listed in the dataset by the AffyID.
Correction to my previous post: only the Genotyping data is available in a basket, for the Exome data it has to be all within the RAP.
Hello, if I want to match the rsID of Exome data(pVCF) with EID, how can I achieve this?
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