Entering edit mode
4.2 years ago
gitanjali.tandon
•
0
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
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