I am trying to combine two VCF files. The first VCF contains data from genotyping-by-sequencing (low coverage) and variants were called with another software (TASSEL). This first VCF has FORMAT fields GT:AD:DP:GQ:PL.
The second VCF was generated by running GenotypeGVCF using the first VCF as the --intervals file. Basically, I am calling the sites from my first VCF out of the whole-genomes contained in the GVCF. I then run CombineVariants on the two VCFs to get the union of both sets of samples.
My problem is that the GenotypeGVCF contains GT:AD:DP:RGQ. There is no more PL field. My guess is that this happened since I used the --includeNonVariantSites option, which was necessary since many sites in my VCF are not variant in the GVCF.
When I CombineVariants I get the union of FORMAT fields. So the samples from the first VCF have PL, those from the GVCF do not. I now want to do imputation (probably with Beagle) and take advantage of the information contained in the genotype likelihoods. Beagle uses the PL field, so the samples without PL would force me to use the GT fields. Using the GT is not okay because Beagle would use that field even for the low coverage data where you might call a homozygote with just one read.
So how can I get PL out of GenotypeGVCF in my situation OR how can I calculate PL, or re-calculate all PL's from the read depth information in the combined VCF?
Thanks in advance!!
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.
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.
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)
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?
I used Beagle to phase my data but for some indels, I have some probleme :
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?