Question: Beagle Error Reading in .PL file
0
gravatar for karl.fetter
13 months ago by
karl.fetter0 wrote:

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

beagle phasing genome • 424 views
ADD COMMENTlink written 13 months ago by karl.fetter0
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