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, 18:01, 19 May 2015
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| We will start with a set of short sequence reads and associated base quality scores (stored in a fastq file), find the most likely genomic location for each read (producing a BAM file), generate an initial list of polymorphic sites and genotypes (stored in a VCF file) and use haplotype information to refine these genotypes (resulting in an updated VCF file). | | We will start with a set of short sequence reads and associated base quality scores (stored in a fastq file), find the most likely genomic location for each read (producing a BAM file), generate an initial list of polymorphic sites and genotypes (stored in a VCF file) and use haplotype information to refine these genotypes (resulting in an updated VCF file). |
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− | '''Note:''' if you are interested in ''de novo'' mutations or are working on families with deep sequence data, you should also consider our sister program, [http://genome.sph.umich.edu/wiki/Polymutt Polymutt], which ignores linkage disequilibrium information but can handle more complex pedigrees.
| + | === Note === |
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| + | If you are interested in ''de novo'' mutations or are working on one or two families with deep sequence data (>30X), you should first consider our sister program, [http://genome.sph.umich.edu/wiki/Polymutt Polymutt], which ignores linkage disequilibrium information but can handle more complex pedigrees. |
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| === Download === | | === Download === |
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| Before downloading the program, we appreciate if you could email [mailto:weichen.mich@gmail.com weichen.mich@gmail.com] (Subject: TrioCaller, with/without a little descriptive information (e.g. Affiliation, depth, the number of samples and family structure). We will notify you if there is any update. | | Before downloading the program, we appreciate if you could email [mailto:weichen.mich@gmail.com weichen.mich@gmail.com] (Subject: TrioCaller, with/without a little descriptive information (e.g. Affiliation, depth, the number of samples and family structure). We will notify you if there is any update. |
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− | <br> Binary file only: [http://www.sph.umich.edu/csg/weich/TrioCaller.06262012.binary.tgz TrioCaller.06262012.binary.tgz]. | + | '''A recent extension of TrioCaller: [http://genome.sph.umich.edu/wiki/FamLDCaller FamLDCaller] is coming soon with major updates (better processing function, handling general families and reference panels). Please try the beta version below. Contact weichen.mich@gmail.com for any questions.''' |
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| + | [[Binary file:]] [http://www.pitt.edu/~wec47/Files/FamLDCaller FamLDCaller]. [Last update: 08/15/2014] |
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| + | '''TrioCaller''' : the version we used in the paper. |
| + | <br> |
| + | [[Binary file only:]] [http://csg.sph.umich.edu/weich/TrioCaller.06262012.binary.tgz TrioCaller.06262012.binary.tgz]. |
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− | Binary file with example datasets : [http://www.sph.umich.edu/csg/weich/TrioCaller.06262012.tgz TrioCaller.06262012.tgz]. | + | [[Binary file with example datasets :]] [http://csg.sph.umich.edu/weich/TrioCaller.06262012.tgz TrioCaller.06262012.tgz]. |
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| [http://genome.sph.umich.edu/wiki/TrioCaller:Archive Archive]. | | [http://genome.sph.umich.edu/wiki/TrioCaller:Archive Archive]. |
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| + | ''' |
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| + | == An example from sequence data to genotypes == |
| + | ''' |
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| The example dataset demonstrated here is also included. Our dataset consists of 40 individuals, including 10 parent-offspring trios and 10 unrelated individuals. The average sequence depth is ~3x. README.txt describes the structure of the package. Pipeline.csh (C shell) and pipeline.bash (bash shell) are two scripts for you to run all commands listed here in batch. | | The example dataset demonstrated here is also included. Our dataset consists of 40 individuals, including 10 parent-offspring trios and 10 unrelated individuals. The average sequence depth is ~3x. README.txt describes the structure of the package. Pipeline.csh (C shell) and pipeline.bash (bash shell) are two scripts for you to run all commands listed here in batch. |