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freeseek / gtc2vcf

Tools to convert Illumina IDAT/BPM/EGT/GTC and Affymetrix CEL/CHP files to VCF
MIT License
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Error while running linsolve1 #70

Open teepean opened 4 months ago

teepean commented 4 months ago

I have a dataset that I am trying to convert to gtc but ran in to an error using bcftools and idat2gtc version 1.20. GEO accession is GSM5579064 and an example that works on the same dataset GSM5579063.

bcftools +idat2gtc --bpm GSA-24v2-0_A1.bpm --egt GSA-24v2-0_A1_ClusterFile.egt --idats error/ --output gtc/

idat2gtc 2024-05-05 https://github.com/freeseek/gtc2vcf

Using normalization algorithm version 1.2.0

Reading BPM file GSA-24v2-0_A1.bpm

Reading EGT file GSA-24v2-0_A1_ClusterFile.egt

Using genotyping algorithm version 7.0.0

Gender estimation parameters

    Version: 2

    MinX_Loci: 20

    X_HetRateThreshold: 0.100000

    MinAutosomalLoci: 100

    MaxAutosomalLoci: 10000

    MinY_Loci: 20

    AutosomalCallRateThreshold: 0.000000

    X_IntensityThreshold: 0.900000

    Y_IntensityThreshold: 0.300000

Reading GRN IDAT file error//GSM5579064_204425730099_R01C01_Grn.idat

Reading RED IDAT file error//GSM5579064_204425730099_R01C01_Red.idat

Normalizing...

Error while running linsolve1

teepean commented 4 months ago

Looks like using GSA-24v1 fixed this problem.