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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
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://csg.sph.umich.edu//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
minDepth and maxDepth are the cutoffs on total depth (across all individuals). We have found it useful to exclude sites with extremely low and high total depth. Please see Important Filters below.
minDepth and maxDepth are the cutoffs on total depth (across all individuals). We have found it useful to exclude sites with extremely low and high total depth. Please see Important Filters below.
=== (step 2) Genotype/haplotype calling using thunder [https://www.sph.umich.edu/csg/yli/thunder/thunder.V010.source.tgz thunder_glf_freq] ===
=== (step 2) Genotype/haplotype calling using thunder [https://csg.sph.umich.edu//yli/thunder/thunder.V011.source.tgz thunder_glf_freq] ===
thunder_glf_freq --shotgun my.out.$chr --detailedInput -r 100 --states 200 --dosage --phase --interim 25 -o my.final.out
thunder_glf_freq --shotgun my.out.$chr --detailedInput -r 100 --states 200 --dosage --phase --interim 25 -o my.final.out
Notes:
Notes:
(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].
(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://sph.umich.edu/csg/abecasis/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/thunder.V010.source.tgz thunder_glf_freq].
(2) Check out example files and command lines under examples/thunder/ in the thunder package [https://sph.umich.edu/csg/abecasis/thunder/thunder.V011.source.tgz thunder_glf_freq].
== Example Showing the Whole Pipeline ==
In the thunder [https://csg.sph.umich.edu//yli/thunder/thunder.V011.source.tgz thunder_glf_freq] tarball, you can find under example/thunder/ folder, input files extracted from real data and a C-shell script that executes the whole analysis pipeline.
== Ligate Haplotypes ==
== Ligate Haplotypes ==
Please use [http://www.sph.umich.edu/csg/yli/ligateHap.V004.tgz ligateHaplotypes].
Please use [http://csg.sph.umich.edu//yli/ligateHap.V004.tgz ligateHaplotypes].
== Important Filters ==
== Important Filters ==
