Question: How to convert and annotate apt-probeset-genotype into PLINK format
1
gravatar for Myosotis1979
4.9 years ago by
Myosotis197910
Tunisia
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 • 2.8k views
ADD COMMENTlink modified 4 months ago by gitanjali.tandon0 • written 4.9 years ago by Myosotis197910

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

ADD REPLYlink modified 4 months ago by Kevin Blighe69k • written 4 months ago by gitanjali.tandon0

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

G/G

APT is no longer supported (I think)

ADD REPLYlink modified 4 months ago • written 4 months ago by Kevin Blighe69k

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

ADD REPLYlink written 4 months ago by gitanjali.tandon0

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

ADD REPLYlink written 4 months ago by Kevin Blighe69k
1
gravatar for Kevin Blighe
3.3 years ago by
Kevin Blighe69k
Republic of Ireland
Kevin Blighe69k 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.

Kevin

ADD COMMENTlink modified 2.3 years ago by _r_am32k • written 3.3 years ago by Kevin Blighe69k
0
gravatar for freeseek
12 months ago by
freeseek120
freeseek120 wrote:

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

ADD COMMENTlink written 12 months ago by freeseek120
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 972 users visited in the last hour
_