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Jump to navigationJump to searchPolymutt: a tool for calling polymorphism and de novo mutations in families for sequencing data (view source)
Revision as of 15:47, 1 June 2011
, 15:47, 1 June 2011Created page with '== Introduction == * The program '''polymutt''' implemented a likelihood-based framework for calling '''single nucleotide variants''' and detecting '''''de novo''''' '''point mu…'
== Introduction ==
* 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.
* 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)).
* Since unrelated individuals are kind of special case of families, unrelated individuals or a mixture of related and unrelated individuals can be handled.
* 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.
* See below for more details.
== Usage ==
A command without any input will display the basic usage
polymutt
The following parameters are in effect:
pedfile : (-pname)
datfile : (-dname)
glfIndexFile : (-gname)
cutoff : 0.500 (-c99.999)
Additional Options
Map Quality Filter : --minMapQuality
Depth Filter : --minDepth, --maxDepth,
--minPercSampleWithData [0.00]
Scaled mutation rate : --theta [1.0e-03]
Optimization precision : --prec [1.0e-04]
de novo mutation : --denovo, --rate_denovo [0.00],
--tstv_denovo [0.50], --min_denovo_LLR [0.00]
Output : --vcf [variantCalls.vcf]
Multiple threading : --nthreads [1]
An example command for variant calling looks like the following:
polymutt -p in.ped -d in.dat -g glfIndexFile --vcf out.vcf --nthreads 4
An example command for ''de novo'' mutation detection is as follows:
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
== Input files ==
Required input files are -p input.ped -d input.dat -g glfIndex files
* An example in.ped file looks like the following:
fam1 p1 0 0 1 1
fam1 p2 0 0 2 2
fam1 p3 p1 p2 1 3
fam2 p4 0 0 1 4
fam2 p5 0 0 2 5
fam2 p6 p4 p5 1 6
...
* 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):
T GLF_Index
* 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.
1 /home/me/sample1.glf
2 /home/me/sample2.glf
3 /home/me/sample3.glf
4 /home/me/sample4.glf
...
* 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
* 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.
== Other options ==
Some of command line options are explained below and others are self-explanatory.
-c : minimum cutoff of posterior probability to output a variant
--theta : scaled mutation rate per site
--nthreads : number of threads to run and it is recommended to use 4 threads for small number of input files.
--de_novo : a boolean flag to turn on ''de novo'' mutation detection. The following options take effect only when this flag is ON
--rate_denovo : mutation rate per haplotype per generation. Usually it is on the order of 1e-08
--tstv_denovo : the prior ts/tv ratio of ''de novo'' mutations
--min_denovo_LLR : minimum value of log10 likelihood ratio of allowing vs. disallowing ''de novo'' mutations in the data to output
== Output files ==
* The output file is a VCF file and the specification can be found [[http://www.1000genomes.org/node/101 here]]
* 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.
* A summary about variant calling statistics is output to STDOUT and it may be redirected to a file for a record.
Summary of reference -- 9
Total Entry Count: 141213431
Total Base Cout: 120124735
Total '0' Base Count: 137
Non-Polymorphic Count: 655457
Transition Count: 6556
Transversion Count: 3127
Other Polymorphism Count: 0
Filter counts:
minMapQual 4550
minTotalDepth 1089
maxTotalDepth 736
Hard to call: 0
Skipped bases: 134
== Creation of GLF files ==
* 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.
** Download a modified version of samtools ( [[https://github.com/statgen/samtools-0.1.7a-hybrid samtools-hybrid]] )
** Prepare the reference genome in fasta format and sequence alignments in [[http://samtools.sourceforge.net/ SAM/BAM]] format
** Generate BAQ adjusted GLF files using the following command
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
* For other functionalities please refer to the [[http://samtools.sourceforge.net/ samtools]] website.
== Download ==
The pre-compiled 64-bit binary executable for linux with test files can be [[Media:polymutt.tar.gz | downloaded]] here . Source code will be available to download soon.
== Contact ==
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])
* 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.
* 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)).
* Since unrelated individuals are kind of special case of families, unrelated individuals or a mixture of related and unrelated individuals can be handled.
* 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.
* See below for more details.
== Usage ==
A command without any input will display the basic usage
polymutt
The following parameters are in effect:
pedfile : (-pname)
datfile : (-dname)
glfIndexFile : (-gname)
cutoff : 0.500 (-c99.999)
Additional Options
Map Quality Filter : --minMapQuality
Depth Filter : --minDepth, --maxDepth,
--minPercSampleWithData [0.00]
Scaled mutation rate : --theta [1.0e-03]
Optimization precision : --prec [1.0e-04]
de novo mutation : --denovo, --rate_denovo [0.00],
--tstv_denovo [0.50], --min_denovo_LLR [0.00]
Output : --vcf [variantCalls.vcf]
Multiple threading : --nthreads [1]
An example command for variant calling looks like the following:
polymutt -p in.ped -d in.dat -g glfIndexFile --vcf out.vcf --nthreads 4
An example command for ''de novo'' mutation detection is as follows:
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
== Input files ==
Required input files are -p input.ped -d input.dat -g glfIndex files
* An example in.ped file looks like the following:
fam1 p1 0 0 1 1
fam1 p2 0 0 2 2
fam1 p3 p1 p2 1 3
fam2 p4 0 0 1 4
fam2 p5 0 0 2 5
fam2 p6 p4 p5 1 6
...
* 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):
T GLF_Index
* 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.
1 /home/me/sample1.glf
2 /home/me/sample2.glf
3 /home/me/sample3.glf
4 /home/me/sample4.glf
...
* 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
* 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.
== Other options ==
Some of command line options are explained below and others are self-explanatory.
-c : minimum cutoff of posterior probability to output a variant
--theta : scaled mutation rate per site
--nthreads : number of threads to run and it is recommended to use 4 threads for small number of input files.
--de_novo : a boolean flag to turn on ''de novo'' mutation detection. The following options take effect only when this flag is ON
--rate_denovo : mutation rate per haplotype per generation. Usually it is on the order of 1e-08
--tstv_denovo : the prior ts/tv ratio of ''de novo'' mutations
--min_denovo_LLR : minimum value of log10 likelihood ratio of allowing vs. disallowing ''de novo'' mutations in the data to output
== Output files ==
* The output file is a VCF file and the specification can be found [[http://www.1000genomes.org/node/101 here]]
* 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.
* A summary about variant calling statistics is output to STDOUT and it may be redirected to a file for a record.
Summary of reference -- 9
Total Entry Count: 141213431
Total Base Cout: 120124735
Total '0' Base Count: 137
Non-Polymorphic Count: 655457
Transition Count: 6556
Transversion Count: 3127
Other Polymorphism Count: 0
Filter counts:
minMapQual 4550
minTotalDepth 1089
maxTotalDepth 736
Hard to call: 0
Skipped bases: 134
== Creation of GLF files ==
* 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.
** Download a modified version of samtools ( [[https://github.com/statgen/samtools-0.1.7a-hybrid samtools-hybrid]] )
** Prepare the reference genome in fasta format and sequence alignments in [[http://samtools.sourceforge.net/ SAM/BAM]] format
** Generate BAQ adjusted GLF files using the following command
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
* For other functionalities please refer to the [[http://samtools.sourceforge.net/ samtools]] website.
== Download ==
The pre-compiled 64-bit binary executable for linux with test files can be [[Media:polymutt.tar.gz | downloaded]] here . Source code will be available to download soon.
== Contact ==
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])
