Question: How to filter Michigan genotype imputation results
0
gravatar for robjohn70000
12 weeks ago by
robjohn70000110
Nigeria
robjohn70000110 wrote:

Hi,

I have just downloaded imputation result files from the Michigan Imputation Server. The files include ".info.gz" and ".dosage.gz". I will like to filter the genotype results by R^2 > 0.8 to obtain good quality imputed genotypes. I'm new to this kind of analysis and not sure how to proceed from here. Can someone please advise me on how to do this?

Here is .info example:

SNP     REF(0)  ALT(1)  ALT_Frq MAF     AvgCall Rsq     Genotyped       LooRsq  EmpR    EmpRsq  Dose0   Dose1
1:62246 C       T       0.30621 0.30621 0.69406 0.14963 Imputed -       -       -       -       -
1:62209 T       G       0.25723 0.25723 0.75622 0.11694 Imputed -       -       -       -       -

Here is .dosage example:

##fileformat=VCFv4.1
##filedate=2018.4.11
##source=Minimac3
##contig=<ID=10>
##FILTER=<ID=GENOTYPED,Description="Marker was genotyped AND imputed">
##FILTER=<ID=GENOTYPED_ONLY,Description="Marker was genotyped but NOT imputed">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DS,Number=1,Type=Float,Description="Estimated Alternate Allele Dosage : [P(0/1)+2*P(1/1)]">
##FORMAT=<ID=GP,Number=3,Type=Float,Description="Estimated Posterior Probabilities for  Genotypes 0/0, 0/1 and 1/1 ">
##INFO=<ID=AF,Number=1,Type=Float,Description="Estimated Alternate Allele Frequency">
##INFO=<ID=MAF,Number=1,Type=Float,Description="Estimated Minor Allele Frequency">
##INFO=<ID=R2,Number=1,Type=Float,Description="Estimated Imputation Accuracy">
##INFO=<ID=ER2,Number=1,Type=Float,Description="Empirical (Leave-One-Out) R-square (available only for genotyped variants)">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT Sample1 Sample2

However, column "INFO" that contains R2 in the dosage file has this format:

AF=0.00036;MAF=0.00036;R2=0.00035
AF=0.08734;MAF=0.08734;R2=0.18100
imputation qc rsq gwas • 316 views
ADD COMMENTlink modified 6 weeks ago by GK161030 • written 12 weeks ago by robjohn70000110

what does it look like. Provide an example.

ADD REPLYlink written 12 weeks ago by Pierre Lindenbaum109k
0
gravatar for GK1610
6 weeks ago by
GK161030
United States
GK161030 wrote:

try this

file=dosage.vcf.gz

bcftools view -i 'R2>.8' -Oz $file > $file.filtered.vcf.gz; tabix -p vcf $file.filtered.vcf.gz;

ADD COMMENTlink written 6 weeks ago by GK161030
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