convert minimac3 dosages into beds using gcta.

njbern
New Member

Posts: 4

convert minimac3 dosages into beds using gcta. Feb 11, 2016 16:55:51 GMT

Quote

Post by njbern on Feb 11, 2016 16:55:51 GMT

Hi all,

I'm trying to convert minimac3 dosages into beds using gcta. I know this is most likely a trivial problem, but I can't figure it out 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,

Last Edit: Feb 11, 2016 17:03:08 GMT by njbern

njbern New Member Posts: 4	convert minimac3 dosages into beds using gcta. Feb 16, 2016 15:44:15 GMT Quote Select Post Deselect Post Link to Post Member Give Gift Back to Top Post by njbern on Feb 16, 2016 15:44:15 GMT I still have not found a solution any help would be much appreciated. Please

Jian Yang
Administrator

Posts: 362

convert minimac3 dosages into beds using gcta. Feb 17, 2016 5:34:06 GMT

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Post by Jian Yang on Feb 17, 2016 5:34:06 GMT

I've added the required file formats for this option in gcta.freeforums.net/thread/270/input-output

The --dosage-mach option was designed to read output files from an early version of MACH, which might not be compatible with output files from the latest version of MACH or Minimac.

One possible solution is to re-format the *.mlinfo file using awk.

Last Edit: Feb 17, 2016 5:34:32 GMT by Jian Yang

njbern
New Member

Posts: 4

convert minimac3 dosages into beds using gcta. Feb 17, 2016 18:38:17 GMT

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Post by njbern on Feb 17, 2016 18:38:17 GMT

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"_"$3"_"++i' > t && mv t chr$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

This is janky but works

Post by njbern on Feb 11, 2016 16:55:51 GMT

Post by njbern on Feb 16, 2016 15:44:15 GMT

Post by Jian Yang on Feb 17, 2016 5:34:06 GMT

Post by njbern on Feb 17, 2016 18:38:17 GMT