Question: How to convert and annotate apt-probeset-genotype into PLINK format
gravatar for Myosotis1979
3.3 years ago by
Myosotis197910 wrote:

Dear all,

I called SNP genotypes of 100 Affy6 CEL files using apt-probeset-genotype from APT in order to perform a subsequent CNV analysis with PennCNV. As PennCNV doesn't integrate SNP quality control procedure (move out SNP with genotype call < 95%, ...), I need to convert the apt-probeset-genotype output files to PLINK to perform this QC step. Many thanks ......  

penncnv cnv plink snp affymetrix6 • 1.8k views
ADD COMMENTlink modified 21 months ago by Kevin Blighe44k • written 3.3 years ago by Myosotis197910
gravatar for Kevin Blighe
21 months ago by
Kevin Blighe44k
Kevin Blighe44k wrote:

'apt' is obviously Affymetrix Power Tools, right?

Have you looked at the apt-format-result plugin for APT, which converts your TXT output to VCF or PLINK format?

If that doesn't work, please paste a section of your data and I will show you how to convert it to PLINK format manually.


ADD COMMENTlink modified 9 months ago by RamRS22k • written 21 months ago by Kevin Blighe44k
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