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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.  

== Input Data ==

== Input Data ==

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].  

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:  

   samtools pileup -g -T 1 -f ref.fa my.bam > my.glf

   samtools pileup -g -T 1 -f ref.fa my.bam > my.glf

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.  

== How to Run ==

== How to Run ==

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.  

(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].  

   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  

(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].  

   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

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].  

 

(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].  

== Important Filters ==

== Important Filters ==