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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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vcf file blank #54

Closed dtzhu337 closed 9 months ago

dtzhu337 commented 1 year ago

code

bcftools +affy2vcf \ --csv Axiom_UKB_WCSG.na35.annot.csv \ --fasta-ref grc38_ref.fasta \ --calls AxiomGT1.calls.txt \ --confidences AxiomGT1.confidences.txt \ --summary AxiomGT1.summary.txt \ --snp AxiomGT1.snp-posteriors.txt \ -Oz \ --output batch1.vcf.gz

output

affy2vcf 2022-12-21 https://github.com/freeseek/gtc2vcf Reading CSV file Axiom_UKB_WCSG.na35.annot.csv Reading SNP posteriors file AxiomGT1.snp-posteriors.txt Writing VCF file Lines total/missing-reference/missing-snp-posteriors/skipped: 836727/0/0/836727

Hi there, I have generated txt files from apt-genotype-axiom function and confirmed the files are not blank. but when I used the previous code to generate vcf files, the vcf file only contains header with no content. How can I solve this?

Thank you

dtzhu337 commented 1 year ago

I also attached -v parameter to the code, and these are several lines.

Skipping unlocalized marker AX-38110825 Skipping unlocalized marker AX-90031845 Skipping unlocalized marker AX-33599403 Skipping unlocalized marker AX-39071359 Skipping unlocalized marker AX-83108440 Skipping unlocalized marker AX-13320474 Skipping unlocalized marker AX-38259287 Skipping unlocalized marker AX-37884095 Skipping unlocalized marker AX-40475603