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| This page documents how to perform variant calling from low-coverage sequencing data using glfmultiples and thunder. The pipeline was originally developed by [mailto:yunli@med.unc.edu Yun Li] for the 1000 Genomes Low Coverage Pilot Project. | | This page documents how to perform variant calling from low-coverage sequencing data using glfmultiples and thunder. The pipeline was originally developed by [mailto:yunli@med.unc.edu Yun Li] for the 1000 Genomes Low Coverage Pilot Project. |
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− | == Input Data == | + | == Input Data == |
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− | To get started, you will need glf files in the standard format [http://samtools.sourceforge.net/SAM1.pdf glf format]. Sample files are available at [ftp://share.sph.umich.edu/1000genomes/pilot1/examples/glf.tgz sample glf files]. | + | To get started, you will need glf files in the standard format [http://samtools.sourceforge.net/SAM1.pdf glf format]. Sample files are available at [ftp://share.sph.umich.edu/1000genomes/pilot1/examples/glf.tgz sample glf files]. |
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− | If you do not have glf files, you can generate them from bam files (bam format also specified in [http://samtools.sourceforge.net/SAM1.pdf glf format bam format]) using the following command line: | + | If you do not have glf files, you can generate them from bam files (bam format also specified in [http://samtools.sourceforge.net/SAM1.pdf glf format bam format]) using the following command line: |
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− | samtools pileup -g -T 1 -f ref.fa my.bam > my.glf | + | samtools pileup -g -T 1 -f ref.fa my.bam > my.glf |
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− | Note: you will need the reference fasta file ref.fa to create glf file from bam file. | + | Note: you will need the reference fasta file ref.fa to create glf file from bam file. |
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− | == How to Run == | + | == How to Run == |
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− | This variant calling pipeline has two steps. (step 1) promotion of a set of potential polymorphisms; and (step 2) genotype/haplotype calling using LD information. | + | This variant calling pipeline has two steps. (step 1) promotion of a set of potential polymorphisms; and (step 2) genotype/haplotype calling using LD information. |
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− | (step 1) Site promotion using software glfMultiples [https://www.sph.umich.edu/csg/yli/GPT_Freq.011.source.tgz GPT_Freq]. | + | (step 1) Site promotion using software glfMultiples [https://www.sph.umich.edu/csg/yli/GPT_Freq.011.source.tgz GPT_Freq]. |
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| GPT_Freq -b my.out -p 0.9 --minDepth 10 --maxDepth 1000 *.glf | | GPT_Freq -b my.out -p 0.9 --minDepth 10 --maxDepth 1000 *.glf |
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− | (step 2) Genotype/haplotype calling using thunder [https://www.sph.umich.edu/csg/yli/thunder.V009.source.tgz thunder_glf_freq]. | + | (step 2) Genotype/haplotype calling using thunder [https://www.sph.umich.edu/csg/yli/thunder.V009.source.tgz thunder_glf_freq]. |
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| thunder_glf_freq --shotgun my.out.$chr -r 100 --states 200 --dosage --phase --interim 25 -o my.final.out | | thunder_glf_freq --shotgun my.out.$chr -r 100 --states 200 --dosage --phase --interim 25 -o my.final.out |
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| Note: | | Note: |
− | (1) The program thunder used in step 2 is an extension of MaCH, the genotype imputation software we have previously developed. For details regarding the shared options, please check out [http://www.sph.umich.edu/csg/yli/mach/index.html MaCH website] and [http://genome.sph.umich.edu/wiki/Mach MaCH wiki]. | + | |
− | (2) Check out example files and command lines under examples/thunder/ in the thunder package [https://www.sph.umich.edu/csg/yli/thunder.V009.source.tgz thunder_glf_freq]. | + | (1) The program thunder used in step 2 is an extension of MaCH, the genotype imputation software we have previously developed. For details regarding the shared options, please check out [http://www.sph.umich.edu/csg/yli/mach/index.html MaCH website] and [http://genome.sph.umich.edu/wiki/Mach MaCH wiki]. |
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| + | (2) Check out example files and command lines under examples/thunder/ in the thunder package [https://www.sph.umich.edu/csg/yli/thunder.V009.source.tgz thunder_glf_freq]. |
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| == Important Filters == | | == Important Filters == |