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835 bytes added, 12:08, 21 February 2017
(step 2) Genotype/haplotype calling using thunder thunder_glf_freq
This page documents how to perform variant calling from low-coverage sequencing data using glfmultiples and thunder. The pipeline was originally developed by [ Yun Li] and for [ Goncalo Abecasis] the 1000 Genomes Low Coverage Pilot Project.
== Input Data ==
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.
== 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.
=== (step 1) Site promotion using software glfMultiples [ GPT_Freq] ===
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.
=== (step 2) Genotype/haplotype calling using thunder [ thunder_glf_freq] ===
thunder_glf_freq --shotgun my.out.$chr --detailedInput -r 100 --states 200 --dosage --phase --interim 25 -o
(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 [ MaCH website] and [ MaCH wiki].
(2) Check out example files and command lines under examples/thunder/ in the thunder package [ thunder_glf_freq]. == Example Showing the Whole Pipeline ==In the thunder [ 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 ==Please use [ ligateHaplotypes].
== Important Filters ==
=== allelic imbalance ===
A statistic developed by Dr. Tom Blackwell [ allelic imbalance].
=== indel filter ===
We recommend distance to known indels >= 5bp. A catalog of known indels can be found at [ indel catalog].
=== site promotion filter ===
We recommend setting parameter -p at least >= 0.9 in step 1 (running glfMultiples).
=== strand bias filter ===
=== total depth filter ===
=== flanking sequence filter ===
We recommend excluding sites with >0.1% flanking 10-mer frequency among candidate sites. samtools calmd -br performs this base quality re-calibration.
The rationale is == Citation ==Li Y, Sidore C, Kang HM, Boehnke M, Abecasis GR.Low-coverage sequencing: Implications for design of complex trait association studies.<em>Genome Res.</em> 2011 Jun;21(6):940-51.<br>
==Inference with External Reference = indel filter ===We recommend distance to known indels >= 5bp. A catalog of known indels can be found at [ indel catalog].
=== site promotion filter ===We recommend setting parameter -p at least >= 0Please refer to [http://genome.sph.umich.9 in step 1 (running glfMultiples)edu/wiki/UMAKE UMAKE].<br>
== Questions and Comments? ==
Email [ Yun Li].

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