How to convert and annotate apt-probeset-genotype into PLINK format

Question

[Myosotis1979]

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

[gitanjali.tandon]

Dear all,

I am using apt-format-result for converting axiom snp array data into PLINK format.

My call file is in the following format:

probeset_id      1.CEL_call_code   100.CEL_call_code  101.CEL_call_code   Affy_SNP_ID    Chr_id     Start     Strand    dbSNP_RS_ID
AX-156983888    G/G                              G/G                        G/G             Affx-257758710  2147483648  1412      +
AX-159952323    C/C                               T/C                         T/C          Affx-257772378   2147483648   730       +        
AX-161040628    C/C                              C/C                        C/C        Affx-257726202   2147483648   2014     +          
AX-161069234    G/G                              A/G                        G/G       Affx-257752194   2147483648    3019     +         
AX-164911815    C/C                              C/C                         ---           Affx-257786385   2147483648   2000     +

The commands which I am using is : apt-format-result --calls-file calls.csv --annotation-file Axiom.db --export-plink-file new

new.ped and new.map files are formed but are empty.

new.ped being formed is following:

Sample Filename Genotypes
probeset_id,1.CEL_call_code,100.CEL_call_code,101.CEL_call_code,11.CEL_call_code,12.CEL_call_code,126.CEL_call_code,127.CEL_call_code,128.CEL_call_code,129.CEL_call_code,13.CEL_call_code,134.CEL_call_code,136.CEL_call_code,14.CEL_call_code,15.CEL_call_code,16.CEL_call_code,17.CEL_call_code,18.CEL_call_code,19.CEL_call_code,2.CEL_call_code,20.CEL_call_code,21.CEL Affy_SNP_ID,Chr_id,Start,Strand

new.map:
##calls-file=call_check.csv
##annotation-file=Axiom.db
##export-plink-map-file=check.map
#Chromosome Marker ID   Genetic distance    Physical position

Can anyone please help in rectifying this problem. Regards, Geet

[Kevin Blighe]

Are you sure that the genotypes should be encoded this way:

G/G

APT is no longer supported (I think)

[gitanjali.tandon]

THANK YOU FOR THE REPLY.. Yes the data provided to me is in this format only..

[Kevin Blighe]

Please consult the required input format(s) for apt-format-result

[barroyo]

Hi all, I have a related question. Where can I find the annotation file? In this case "Axiom.db" was used but I can't find anything similar in my library files. Should this be supplied by APT? or is this an output from any steps of the APT QC workflow? Kind regards, B

[Kevin Blighe]

Question asked at: https://support.bioconductor.org/p/9143017/

Answer 1

[Kevin Blighe]

'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.

Kevin

[tvibhaps]

Currently this apt-format-result page (having plugin for APT) redirects the thermofisher webpage as below https://www.thermofisher.com/us/en/home/life-science/microarray-analysis.html? .

I do not find the apt-format-result page anymore. Not sure where to find it. Thanks.

Vibha

Answer 2

[Giulio Genovese]

You can use the affy2vcf bcftools plugin to convert the apt-probeset-genotype output to VCF and then use best practices to convert the VCF output to PLINK format or easily perform the quality control on the VCF file using bcftools