ANGSD: Analysis of next generation Sequencing Data
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Beagle input: Difference between revisions
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NBNB: The information on this page refers to version 3 of beagle. | |||
Beagle haplotype imputation can be performed directly on genotype likelihoods. To generate beagle input file use | Beagle haplotype imputation can be performed directly on genotype likelihoods. To generate beagle input file use | ||
Latest revision as of 17:53, 6 November 2017
NBNB: The information on this page refers to version 3 of beagle.
Beagle haplotype imputation can be performed directly on genotype likelihoods. To generate beagle input file use
- -doGlf 2
In order to make this file the major and minor allele has the be inferred (-doMajorMinor) and genotype likelihoods need to be estimated (-GL) . It is also a good idea to only use the polymorphic sites, see Filters and SNP_calling.
Example
In this example our input files are bam files. We use the samtools genotype likelihood methods. We use 10 threads. We infer the major and minor allele from the likelihoods and estimate the allele frequencies. We test for polymorphic sites and only output the ones with are likelhood ratio test p-value<1e-6.
./angsd -GL 1 -out genolike -nThreads 10 -doGlf 2 -doMajorMinor 1 -SNP_pval 1e-6 -doMaf 1 -bam bam.filelist
output
The above command generates the file genolike.beagle.gz that can be use as input for the beagle software
marker allele1 allele2 Ind0 Ind0 Ind0 Ind1 Ind1 Ind1 Ind2 Ind2 Ind2 Ind3 Ind3 Ind3 1_14000023 1 0 0.941177 0.058822 0.000001 0.799685 0.199918 0.000397 0.666316 0.333155 0.000529 1_14000072 2 3 0.709983 0.177493 0.112525 0.941178 0.058822 0.000000 0.665554 0.332774 0.001672 1_14000113 0 2 0.855993 0.106996 0.037010 0.333333 0.333333 0.333333 0.799971 0.199989 0.000040 1_14000202 2 0 0.835380 0.104420 0.060201 0.799685 0.199918 0.000397 0.333333 0.333333 0.333333 ...
Note that the above values sum to one per site for each individuals. This is just a normalization of the genotype likelihoods in order to avoid underflow problems in the beagle software it does not mean that they are genotype probabilities.
The imputation can be done in beagle using the command
java -Xmx15000m -jar beagle.jar like=genolike.beagle.gz out=beagleOutName
Beagle outputs phasing and genotype probabilities. These can be using in ANGSD for downstream analysis such as MAF estimation and Association testing