beagle to gds for admixture mapping
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12 days ago
nanodano ▴ 30

How do you convert dosage beagle files to GDS?

I have local ancestry inference files separated out by the chromosome and inferred ancestry. These files contain dosage information. For example:

zless chr1_anc0_dosage.bgl.gz | cut -f1-5 | head -n 4
I       id      XX100   XX108   XX112
M       rs1000033       0       1       2 
M       rs1000313       0       1       2 
M       rs1000370       0       1       2

I also have marker files for each chromosome, which look like this:

head -n4 chr1.markers.txt 
rs57181708 X874496 A G
rs7518581 899576 G A
rs72890788 901544 G A
rs57494724 901812 A G

I prepared these files for an association study that uses admixture mapping. I'd like to use GENESIS and GWASTools for the analysis, but I'm lost on how to convert these files from bgl to gds. I've tried beagle2vcf

java -jar beagle2vcf.jar 1 chr1.markers.txt chr1_anc0_dosage.bgl.gz > chr1_anc0_dosage.vcf

But the output I got was this:

java -jar beagle2vcf.jar 1 chr1.markers.txt chr1_anc0_dosage.bgl.gz > chr1_anc0_dosage.vcf

beagle2vcf 1.2
usage: java -jar beagle2vcf.jar [chrom] [markers] [bgl] [missing] > [vcf]

where 
  [chrom]   = chromosome identifier in output VCF file.
  [markers] = Beagle version 3 markers file.
  [bgl]     = Beagle version 3 genotypes file.
  [missing] = missing allele code in Beagle genotypes file.
  [vcf]     = output VCF file.

Markers in the markers file and Beagle genotypes file must be identical
and sorted in order of increasing position.  The first allele for a marker
in the markers file will be the REF allele in the output VCF file.  Alleles
in the markers file must contain only 'A', 'C', 'G', and 'T' characters

Is there a better way to do this? Am I messing up somewhere? Any help is greatly appreciated!

admixture genesis gwastools gds beagle • 174 views
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