Question: Merge BEAGLE .gprobs files
1
gravatar for anastazie.d
6.0 years ago by
anastazie.d30
Czech Republic/Prague/HPST
anastazie.d30 wrote:

Hi,

I have two files in BEAGLE .gprobs format containing genotype probabilities for SNPs that I want to merge.

Is there any software that can do that?

Input files:

1. output from ANGSD software, crated using following command:

./angsd -GL 2 -doGlf 2 -bam /media/4TB2/Ngsadmix/bamlist.txt -doMajorMinor 1 -SNP_pval 1e-6 -doMaf -1 -P 16 -out /media/4TB2/Ngsadmix/angsd13102014

2. PLINK file -> beagle file -> beagle .gprobs file

fcgene --ped ket_ngs_all2_plink.ped --map ket_ngs_all2_plink.map --oformat beagle --out ket_ngs_all2_plink_beagle

java -jar ~/Downloads/beagle2gprobs.jar ket_ngs_all2_plink.markers ket_ngs_all2_plink_beagle.bgl N > ket_ngs_all2_plink_beagle.gprobs

Expected output:

Merged file containing both angsd13102014.gprobs and ket_ngs_all2_plink_beagle.gprobs

 

Thanks,

Anastassiya

 

 

 

beagle snp • 2.2k views
ADD COMMENTlink written 6.0 years ago by anastazie.d30
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