Deleted:genotyping affymetrix files
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scipio04 • 0
@a6b1f305
Last seen 3.3 years ago
France

Dear bioinformaticians

im trying to genotype chip seq data file in CEL format , data type : axiom 1920 Axiom Pyrus 70K SNP arrays

I use affymetrix power tool in linux command line , see https://github.com/freeseek/gtc2vcf and

https://www.affymetrix.com/support/developer/powertools/changelog/VIGNETTE-snp6-on-axiom.html#introduction

but when i run the the first step of genotyping , with the standard library file "GenomeWideSNP_6" i have the returning error " Unexpected Error: uncaught exception"

which doesnt indicate me anything about what's wrong

maybe i have to use different library file that fit well with my kind of data but i can't find it on affymetrix database

if you have any idea about this issue , thank you

/apt-probeset-genotype --feat-effects --read-models-brlmmp GenomeWideSNP_6.generic_prior.txt --probeset-ids GenomeWideSNP_6.random.20K.intersect.txt 
--log-file probeset.log --write-models -xml-file GenomeWideSNP_6.apt-probeset-genotype.AxiomGT1.xml --out-dir $output --cel-files $cel --summaries --force


Loading options from file: GenomeWideSNP_6.apt-probeset-genotype.AxiomGT1.xml
 set-analysis-name = AxiomGT1
 chip-type = GenomeWideSNP_6
 analysis = artifact-reduction.ResType=2.Clip=0.4.Close=2.Open=2.Fringe=4.CC=2,quant-norm.target=1000.sketch=50000,pm-only,brlmm-p.CM=1.bins=100.mix=1.bic=2.lambda=1.0.HARD=3.SB=0.75.transform=MVA.copyqc=0.00000.wobble=0.05.MS=0.15.copytype=-1.clustertype=2.ocean=0.00001.CSepPen=0.1.CSepThr=4
 qmethod-spec = med-polish.expon=true
 cdf-file = GenomeWideSNP_6.cdf
 chrX-probes = GenomeWideSNP_6.chrXprobes
 chrY-probes = GenomeWideSNP_6.chrYprobes
 target-sketch = GenomeWideSNP_6.AxiomGT1.sketch
 set-gender-method = cn-probe-chrXY-ratio
 em-gender = false
 female-thresh = 0.54
 male-thresh = 1.0
Unexpected Error: uncaught exception.
ChIPSeq GenotypingArrayData AffymetrixChip • 1.1k views
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