Question: Minimac3 to plink using GCTA
1
gravatar for njbernstein
3.6 years ago by
njbernstein40
United States
njbernstein40 wrote:

Hi all,

I'm trying to convert minimal dosages into beds using gcta. Here's my code:

gcta64  --dosage-mach  chr22.imputed.dose     chr22.imputed.info  --make-bed --out chr22.fdgsdf

My error is:

Reading dosage data failed. Please check the format of the map file.

Here's what my info file looks like:

SNP    REF    ALT    Major    Minor    MAF    AvgCall    Rsq    Genotyped    LooRsq    EmpR    EmpRsq    Dose1    Dose2

22:16050115    G    A    G    A    0.00639    0.99361    0.00000    -    -    -    -    -    -

22:16050213    C    T    C    T    0.00759    0.99241    0.00000    -    -    -    -    -    -

22:16050568    C    A    C    A    0.00040    0.99960    0.00005    -    -    -    -    -    -

22:16050607    G    A    G    A    0.00100    0.99900    0.00002    -    -    -    -    -    -

22:16050627    G    T    G    T    0.00040    0.99960    0.00005    -    -    -    -    -    -

22:16050654    A    <CN0>    A    <CN0>    0.00180    0.99820    0.00000    -    -    -    -    -    -

22:16050654    A    <CN2>    A    <CN2>    0.01737    0.98263    0.00000    -    -    -    -    -    -

Any ideas?

Best,

 

gcta • 1.5k views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by njbernstein40
1
gravatar for njbernstein
3.6 years ago by
njbernstein40
United States
njbernstein40 wrote:

Answer:

for chr in `seq 1 22`;
do
awk -v OFS='\t'  '!($4="") , !($5="")' chr$chr.imputed.info > chr$chr.imputed.info.reworked
sed -i 's/\t\t//' chr$chr.imputed.info.reworked 
awk '{t=$5; $5=$4; $4=t; print}' chr$chr.imputed.info.reworked  > t && mv t chr$chr.imputed.info.reworked
awk '{$6=.999 FS $6;}1' OFS='\t'  chr$chr.imputed.info.reworked > t && mv t chr$chr.imputed.info.reworked
awk '$1=$1"_"$2"_"$3"_"++i' chr$chr.imputed.info.reworked > t && mv t chr$chr.imputed.info.reworked
sed -i '1 s/^.*$/SNP\tAl1\tAl2\tFreq1\tMAF\tAvgCall\tRsq\tGenotyped\tLooRsq\tEmpR\tEmpRsq\tDose1\tDose2/g' chr$chr.imputed.info.reworked

gzip chr$chr.imputed.info.reworked
/labseq/tools/gcta_1.24.2/gcta64  --dosage-mach-gz chr$chr.imputed.dose.gz chr$chr.imputed.info.reworked.gz  --make-bed --out chr$chr.imputed
done

 

ADD COMMENTlink written 3.6 years ago by njbernstein40

Hi thanks for the answer. I'm using GCTA to convert Minimac3 output files as well. Just want to ask have you using filter option to filter out low rsqr genotypes? Using the --dosage-mach command, and adding the filter flag, I found that it actually filter out the wrong column--- the AvgCall rather than R2. Have you encountered a similar problem? Thanks

ADD REPLYlink written 2.8 years ago by xliu425510
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