I need to convert Axiom output to PLINK format I did not find annotation.db

Question

[AlmuhayyaA]

Hi all,

I have .CELL raw data from Axiom Genome-Wide CEU 1 Array Plate https://www.thermofisher.com/order/catalog/product/901608

I got the library from https://www.thermofisher.com/sa/en/home/life-science/microarray-analysis/microarray-data-analysis/genechip-array-library-files.html

I did the genotype calling using this command

 apt-genotype-axiom \
  --analysis-files-path ./AxiomGWAS_HuSNP_1_Analysis-r6/ \
  --cel-files ./cel_list3.txt \
  --out-dir ./output_genotypes \
  --chip-type Axiom_GW_Hu_SNP \
  --spf-file ./AxiomGWAS_HuSNP_1_Analysis-r6/Axiom_GW_Hu_SNP.r6.spf \
  --snp-priors-input-file ./AxiomGWAS_HuSNP_1_Analysis-r6/Axiom_GW_Hu_SNP.r6.generic_prior.txt \
  --dual-channel-normalization true \
  --summaries \
  --write-models \
  --log-file axiom_analysis.log

and I got genotype.call.txt file

I tried to convert this file to PLINK format using this command

apt-format-result \
  --calls-file Axiom_GW_Hu_SNP.calls.txt \
  --annotation-file Axiom_GW_Hu_SNP.na35.annot.csv \
  --export-plink-file axiom_plink

I received error #

ERROR    1 229 | Failed to execute sql statement, load chromosome table failed.    Sql: select key, name, shortname from Chromosome, ErrMsg: Failed to prepare sql statement for querying. SQL: select key, name, shortname from Chromosome, ErrCode: 26 (https://www.sqlite.org/rescode.html), Database Error: file is not a database

that it needs annotation.db instead of annotation.csv how can I get this SQL format db?

[GenoMax]

apt-genotype-axiom

Curious as to what software package are you using here? That beginning apt sounds like package manager command from some linux distros.

Edit: Looks like apt refers to Analysis Power Tools (APT), which is Thermo's software for Axiom arrays.