Entering edit mode
6.8 years ago
karl.fetter
•
0
Hello Biostars,
I am attempting to use beagle to impute missing genotypes. I created a .PL file containing genotypes and likelihood scores for the genotypes using vcftools. I created a single file for each chromosome and named them chr1.BEAGLE.PL, chr2.BEAGLE.PL, etc. I used the following command to initiate phasing:
java -Xss5m -Xmx20g -jar /popgen/beagle/beagle.08Jun17.d8b.jar gtgl=../chromosomes/chr1.BEAGLE.PL out=chr1.phased
and I get the following error messages. These error messages are preceeded by beagle printing all of my sample names to screen.
at vcf.VcfHeader.checkHeaderLine(VcfHeader.java:135)
at vcf.VcfHeader.<init>(VcfHeader.java:119)
at vcf.VcfIt.<init>(VcfIt.java:190)
at vcf.VcfIt.create(VcfIt.java:175)
at vcf.VcfIt.create(VcfIt.java:150)
at main.Main.nonRefData(Main.java:269)
at main.Main.main(Main.java:111)
The input .PL file looks like this:
marker alleleA alleleB CBI_10_R1 CBI_10_R1 CBI_10_R1 CBI_12_R3 CBI_12_R3
1:2078 T G 3.16228e-26 1.58489e-05 1 1 1 1 1 1
1:2126 A G 3.16228e-26 1.58489e-05 1 1 1 1 1 1
1:11785 C T 1 0.0316228 1e-18 1 0.0316228 1e-18 1 0.501187
1:11787 C T 1 0.0316228 1e-18 1 0.0316228 1e-18 1 0.501187
1:11788 T C 1 0.0316228 1e-18 1 0.0316228 1e-18 1 0.501187
1:11789 C T 1 0.0316228 1e-18 0.00794328 1 1.25893e-13 1
1:11790 T C 1 0.0316228 1e-18 1 0.0316228 1e-18 1 0.501187
1:11796 T C 1 0.0316228 1e-18 1 0.0316228 1e-18 1 0.501187
1:11801 A G 1 0.0316228 1e-18 1 0.0316228 1e-18 1 0.501187
Does anyone have experience with beagle or these kinds of error messages and know how to solve these kinds of problems?
Thanks for the tips in advance!
Karl
