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| − | == Updates ==
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| − | The latest version of 0.03 is available for [[#Download | Download ]].
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| − | == Introduction ==
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| − | * The program '''polymutt''' implemented a likelihood-based framework for calling '''single nucleotide variants''' and detecting '''''de novo''''' '''point mutation''' events in families for next-generation sequencing data. The program takes as input genotype likelihood format (GLF) files which can be generated following the [[#Creation of GLF files | Creation of GLF files]] instruction and outputs the result in the [[http://www.1000genomes.org/node/101 VCF]] format. The variant calling and ''de novo'' mutation detection are modelled jointly within families and can handle both nuclear and extended pedigrees without consanguinity loops. The input is a set of GLF files for each of family members and the relationships are specified through the .ped file.
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| − | * The evidence of variants and ''de novo'' mutations are assessed probabilistically. For a variant, the QUAL value is calculated as -10*log10(1-posterior(Variant | Data)) and for ''de novo'' mutation events a ''de novo'' quality (DQ) value is defined as log10(lk_denovo / lk_no_denovo) where lk_denovo and lk_no_denovo are the likelihoods of data allowing and disallowing ''de novo'' mutations respectively. Similarly, for each genotype, a genotype quality (GQ) value is defined as -10*log10(1-posterior(Genotype | Data)).
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| − | * Since unrelated individuals are kind of special case of families, unrelated individuals or a mixture of related and unrelated individuals can be handled.
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| − | * If some individuals in a family are not sequenced, this can be handled by setting the corresponding GLF file indices to zero for those family members who are not sequenced.
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| − | * NOTE: This version only works for autosomes. Variant calling for X, Y and MT is in the testing process and will be available in next version.
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| − | * See below for more details.
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| − | == Usage ==
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| − | A command without any input will display the basic usage
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| − | polymutt
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| − | The following parameters are in effect:
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| − | pedfile : (-pname)
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| − | datfile : (-dname)
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| − | glfIndexFile : (-gname)
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| − | posterior cutoff : 0.500 (-c99.999)
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| − | Additional Options
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| − | Map Quality Filter : --minMapQuality
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| − | Depth Filter : --minDepth, --maxDepth,
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| − | --minPercSampleWithData [0.00]
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| − | Scaled mutation rate : --theta [1.0e-03]
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| − | Prior of ts/tv ratio : --poly_tstv [2.00]
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| − | de novo mutation : --denovo, --rate_denovo [1.5e-08],
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| − | --tstv_denovo [2.00], --minLLR_denovo [1.00]
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| − | Optimization precision : --prec [1.0e-04]
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| − | Multiple threading : --nthreads [1]
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| − | Chromosomes to process : --chr2process []
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| − | Output : --vcf [variantCalls.vcf], --gl_off
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| − | An example command for variant calling looks like the following:
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| − | polymutt -p in.ped -d in.dat -g glfIndexFile --vcf out.vcf --nthreads 4
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| − | An example command for ''de novo'' mutation detection is as follows:
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| − | polymutt -p in.ped -d in.dat -g glfIndexFile --denovo --rate_denovo 1.5e-08 --min_denovo_LLR 1.0 --vcf out.denovo.vcf --nthreads 4
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| − | == Input files ==
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| − | Required input files are -p input.ped -d input.dat -g glfIndex files
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| − | * An example in.ped file looks like the following:
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| − | fam1 p1 0 0 1 1
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| − | fam1 p2 0 0 2 2
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| − | fam1 p3 p1 p2 1 3
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| − | fam2 p4 0 0 1 4
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| − | fam2 p5 0 0 2 5
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| − | fam2 p6 p4 p5 1 6
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| − | ...
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| − | * An example in.dat file is like the following (for the 6th column above and in addition other traits/markers can be specified but will be ignored):
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| − | T GLF_Index
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| − | * An example glfIndex file is like the following and the numbers (except zeros) in the 6th column in the above in.ped file have to be present in the first column.
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| − | 1 /home/me/sample1.glf
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| − | 2 /home/me/sample2.glf
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| − | 3 /home/me/sample3.glf
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| − | 4 /home/me/sample4.glf
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| − | ...
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| − | * If some of the members are not sequenced but are in the pedigree because of the relatedness with other members, the GLF_Index column (6th column) in the ped file should be set to zero
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| − | * For unrelated individuals, you can either (1) create a family for each unrelated individual as a founder or (2) put all unrelated individuals as founders in a single family.
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| − | == Other options ==
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| − | Some of command line options are explained below and others are self-explanatory.
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| − | -c : minimum cutoff of posterior probability to output a variant [''Default: 0.5'']
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| − | --theta : scaled mutation rate per site [''Default: 0.001'']
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| − | --tstv: prior of ts:tv ratio [''Default: 2.0'']
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| − | --nthreads : number of threads to run and it is recommended to use 4 threads for small number of input files [''Default: 1']
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| − | --denovo : a boolean flag to turn on ''de novo'' mutation detection. The following options take effect only when this flag is ON
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| − | --rate_denovo : mutation rate per haplotype per generation. [''Default: 1.5e-08'']
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| − | --tstv_denovo : the prior ts/tv ratio of ''de novo'' mutations. [''Default: 2.0'']
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| − | --minLLR_denovo : minimum value of log10 likelihood ratio of allowing vs. disallowing ''de novo'' mutations in the data to output [''Default: 1.0'']
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| − | --chr2process: the chromosome names to process. Default is empty and is to process all chromosomes in the input.
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| − | If multiple chromosomes are provided, they should be separated by comma, e.g. --chr2process 2,10 or --chr2process chr2,chr10
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| − | --gl_off: not to output genotype likelihood values for each individual. Default is to output 3 GLs for polymorphisms and 10 GLs for de novo mutations
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| − | == Output files ==
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| − | * The output file is a VCF file and the specification can be found [[http://www.1000genomes.org/node/101 here]]
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| − | * Since there is no standard to represent ''de novo'' mutations in the current VCF specification, actual genotypes (e.g. [ACGT]/[ACGT]) are output in the VCF file for ''de novo'' mutations.
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| − | * A summary about variant calling statistics is output to STDOUT and it may be redirected to a file for a record.
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| − | Summary of reference -- 9
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| − | Total Entry Count: 141213431
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| − | Total Base Cout: 120124735
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| − | Total '0' Base Count: 137
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| − | Non-Polymorphic Count: 655457
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| − | Transition Count: 6556
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| − | Transversion Count: 3127
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| − | Other Polymorphism Count: 0
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| − | Filter counts:
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| − | minMapQual 4550
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| − | minTotalDepth 1089
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| − | maxTotalDepth 736
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| − | Hard to call: 0
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| − | Skipped bases: 134
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| − | == Creation of GLF files ==
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| − | * The current version performs variant calling and ''de novo'' mutation detection from files in the genotype likelihood format (GLF). In future versions we plan to take [[http://samtools.sourceforge.net/ SAM/BAM]] files as input. See the following for instructions on how to create GLF files.
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| − | ** Download a modified version of samtools ( [[https://github.com/statgen/samtools-0.1.7a-hybrid samtools-hybrid]] )
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| − | ** Prepare the reference genome in fasta format and sequence alignments in [[http://samtools.sourceforge.net/ SAM/BAM]] format
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| − | ** Generate BAQ adjusted GLF files using the following command
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| − | samtools view -bh chr1.bam 1:0 | samtools calmd -Abr - human.v37.fa 2> /dev/null | samtools pileup - -g -f human.v37.fa > chr1.bam.glf
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| − | * For other functionalities please refer to the [[http://samtools.sourceforge.net/ samtools]] website.
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| − | == Download ==
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| − | The latest version of source code v0.03 with test files can be [[Media:polymutt.0.03.tar.gz | downloaded]] here.
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| − | == Contact ==
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| − | For questions please contact the authors (Bingshan Li: [mailto:bingshan@umich.edu bingshan@umich.edu] or Goncalo Abecasis: [mailto:goncalo@umich.edu goncalo@umich.edu])
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| − | [[Category:Software]]
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