Recently, we imputed our data using https://imputationserver.sph.umich.edu.
However, since the output file format is vcf dosage data, I cannot use Mach2dat for GWAS association analysis.
Does anyone know how to convert vcf dosage file format to mldose format?
Thank you so much!
Dosage file format (mldose for Mach2dat input format):
10009->QZ0526 DOSE 1.997 2.000 1.285 1.997 1.996 1.997 1.994 1.999 0.735 1.750 1.936
10010->QZ0488 DOSE 0.783 0.002 1.996 0.853 0.011 0.791 0.830 1.998 0.930 1.996 1.987
VCF file format from imputation:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT QZ0001 QZ0002 QZ0003 QZ0006
20 60479 20:60479 C T . PASS MAF=0.00078;R2=0.01037 GT:DS 0|0:0.001 0|0:0.009 0|0:0.008 0|0:0.000
20 60522 20:60522 T TC . PASS MAF=0.00249;R2=0.02914 GT:DS 0|0:0.001 0|0:0.002 0|0:0.000 0|0:0.002
1 answer
You can actually do a binary and quantitative GWAS using the michigan server output with SNPTEST if you are open to using different software. https://mathgen.stats.ox.ac.uk/genetics_software/snptest/old/snptest_v2.3.0.html#Support_for_vcf_files note in this example they are using the genotype (GT) versus probability (GP)
Commands are as follows snptest \ -data yourvcf.vcf.gz sample_file.sample \ -genotype_field GP \ -o outputfilename.txt \ -frequentist 1 \ -method score \ -pheno Affected \ -cov_names cov1 cov2 cov3 \ #should you need covariates
Hope this helps
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That VCF would be easily converted to a PLINK .dat file - would that suit your purpose?
Could you be more specific on that? Thank you.
Yeah, could you elaborate more? I only know how to use PLINK to conver to ped file.
Hi I have this problem. Have you solved it? Could you give me the solution?