Entering edit mode
6 weeks ago
AlmuhayyaA
•
0
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?
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 toAnalysis Power Tools (APT)
, which is Thermo's software for Axiom arrays.