Conversion of SNP array data to PLINK format

Question

[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]

Thank you, you also posted here: A: How to convert and annotate apt-probeset-genotype into PLINK format

... and I provided a comment: C: How to convert and annotate apt-probeset-genotype into PLINK format

Answer 1

[Dan]

I think you should be able to adapt this script I wrote:

It uses GEOParse and pandas-plink libraries.