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Created 2015-08-12 06:07:04 | Updated | Tags: beagle haploid-snp-calling
Comments (6)

Hi, I am trying to identify the shared region of genome among several pair of brothers in ant who are haploid. I have run the GATK variant discovery pipeline and currently I have VCF file which have only the Homozygous snps as expected. Now can anyone help me to know whether I can make use of beagle to get the shared/common haplotype information from the pair of brothers.also correct me if I am doing something wrong as I new to this field.

PS as of the VCF is unphased.

Created 2015-08-10 00:02:58 | Updated 2015-08-10 00:14:35 | Tags: haplotypecaller phasing beagle read-backed-phasing
Comments (2)


I have been using HaplotypeCaller 3.4 on five hundred cattle genomes. I am wondering how to pass the physical phasing information, now generated by Haplotype Caller in N+1 mode, through GenotypeGVCF applying pedigree and then out to Beagle 4.0 as a vcf.gz for imputation. My goal is to make a phased reference that is as accurate as possible to be used as an imputation resource. hence I would like to exploit physical phasing information.

Do you have an example work flow? It seems that the recommendations for read-backed phasing have changed since haplotype caller 3.3 came up with the N+1 workflow.



Created 2013-08-08 13:42:13 | Updated | Tags: beagle
Comments (4)


I'm trying to phase GATK genotype and to impute some SNP calls. Before I could do that, I must convert GATK results to an acceptable BEAGLE input format. What's the difference between VariantsToBeagleUnphased and ProduceBeagleInput? I know the latter outputs a file with genotype likelihoods. Incidentally, using that file didn't work in BEAGLE and produced the following log and error files. Can anyone give any pointers? Thanks in advance!

[stechen@node24 ~]$ more beagle_run_410.o720239 Beagle version 3.3.2 (31 Oct 2011) Enter "java -jar beagle.jar" for summary of command line arguments. Start time: 11:59 AM EDT on 07 Aug 2013

Command line: java -Xmx7281m -jar beagle.jar like=beagle_input_410_impute phased=~/stechen/phase_ref/ALL.chr1.phase1_release_v3.20101123.filt.bgl markers=~stechen/phase_ref/ALL.chr1.phase1_release_v3.20101123.filt.markers missing=? out=beagle_output_410_chr1

[stechen@node24 ~]$ more beagle_run_410.e720239 bash: module: line 1: syntax error: unexpected end of file bash: error importing function definition for `module' Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=~stechen/tmp -Xms256m -Xmx8G Exception in thread "main" java.lang.NullPointerException at phaser.y.a(Unknown Source) at phaser.y.(Unknown Source) at phaser.H.a(Unknown Source) at phaser.v.(Unknown Source) at phaser.PhaseMain.(Unknown Source) at phaser.PhaseMain.main(Unknown Source)

Created 2013-01-28 06:08:54 | Updated 2013-01-28 06:18:43 | Tags: producebeagleinput likelihoods beagle community
Comments (1)

Dear GATK team and community members,

I used ProduceBeagleInput to create a genotype likelihoods file, and ran beagle.jar according to the example in http://gatkforums.broadinstitute.org/discussion/43/interface-with-beagle-software. Beagle gave a warning that it is better to use a reference panel for imputing genotypes and phasing. So I downloaded the recommended reference panel (http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes.phase1_release_v3/), but Beagle requires that the alleles be in the same order on both reference and sample files. The tool to do this is check_strands.py (http://faculty.washington.edu/sguy/beagle/strand_switching/README), but it requires both sample and reference files be in .bgl format. This is a little disappointing since not being able to use the reference panel means Beagle's calculations won't be as accurate, although I'm not sure by how much.

I understand that this might be out of the scope of responsibility for the GATK team, but I will greatly appreciate if someone can provide suggestions to allow GATK's input to Beagle be phased using a reference panel. Or hopefully, the GATK team will write a tool to produce .bgl files?

Regards, Jamie

Created 2012-10-23 16:26:23 | Updated 2012-10-23 18:27:35 | Tags: combinevariants phasing beagle
Comments (8)


I used Beagle to phase my data but for some indels, I have some probleme :

example :

Input vcf :

2       68599872        .       ATG     A       14.40   PASS    AC=1;AC1=1;AF=0.028

Input for beagle created by ProduceBeagleInput:

2:68599872 TG - 1.0000 0.0000 0.0000 ......

Output vcf created by BeagleOutputToVCF:

2       68599872        .       ATG     .       14.40   BGL_RM_WAS_-    AC1=1;AF1=0.02965.....

error message by CombineVariants:

MESSAGE: Badly formed variant context at location 68599872 in contig 2. Reference length must be at most one base shorter than location size

Can you help me?