malformed plink files

[Maryiam Shöâeè]

Hi ADNI team members

I converted the WGS (GATK called) vcf.tar files available online to vcf.gz files and then to plink files and started with normal QC. I had to halt the process when running --check-sex on plink generated 430 errors. The only time I have had such issues has been with malformed plink files. I am repeating the process to regenerate the plink files hoping that will solve the problems. 

 

This is what I have done so far: 

1) unzip with tar 

2) zip with tabix tools and produce tbi files

3) merge the files and produce 1 vcf file (interestingly when I tried to produce vcf.gz and the corresponding tbi file for the merged data, there were many errors, so I decided to just proceed with the uncompressed vcf file. 

4) using bcf tools I assign a different ID for multiallelic SNPs and indels: 

bcftools norm -Ou -m -any concatADNI.vcf | 

bcftools norm -Ou -f human_g1k_v37.fasta | 

bcftools annotate -Ob -x ID -I +'%CHROM:%POS:%REF:%ALT' | 

plink --bcf /dev/stdin --keep-allele-order  --vcf-idspace-to _    --const-fid --allow-extra-chr 0  --split-x b37 no-fail  --make-bed  --out output

So my question is this: What do you recommend for converting the GATK aligned vcf files to plink format files if not the above? I am repeating each stage hoping to solve the issues but I doubt it will, so it would be good to know what the recommended alternative is. 

Thanks in advance

Maryiam

 

[Danielle J Harvey]

Hi Maryiam,

 

I don’t work with the genetics data, so can’t help you. If you do not get a response from this group, I’d recommend using the Ask the Experts tool on the ADNI website and direct your question to the Genetics Core (http://adni.loni.usc.edu/support/experts-knowledge-base/ask-experts/) to see if they can answer your questions.

 

Danielle

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[Maryiam Shöâeè]

Thanks I will do.