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...wiki page gives detailed instruction on pre-phasing GWAS data of different samples sizes. This also applies for phasing of the non-Pseudo-Autosomal Region (on ...an resolve long haplotypes in samples of unrelated individuals. The source code is available for download [http://www.sph.umich.edu/csg/abecasis/MaCH/downl

This package contains source code and brief instruction of the method use in the paper by Hu et al, titled "T ...change all the number of random samples from 1e5 (100K) to 1e6 (1M) in the code

...likelihood-based method to prioritize individuals in family AND population samples. Please go to [[RAREFY_DOWNLOAD | '''DOWNLOAD PAGE''']] for source code and executables.

You will use both an <code>VcfFileReader</code> and an <code>VCfRecord</code> for reading VCF files. === <code>VcfFileReader</code> ===

* Section names are specified between square brakets (<code>[]</code>) ...r a key defined in another section, use <code>$(otherSectionName/keyName)</code>

Source code can in: [[Media:vcfRefGen.0.1.4.tgz‎|VcfRefGen.0.1.4.tgz‎]] - Released |style=white-space:nowrap|<code>--in <filename></code>

...ited before PLINK can perform association tests). The <code>OutPrefix.fam</code> will NOT contain sex information unless chromosome X is available. See [[# When <code>--type mach</code> is used, the <code>--format</code> parameter can only take values 1 or 2.

(1) Download the pre-compiled binary along with the source code as described in [[#Binary Download|Binary Download]]. ...[[#Source Code Distribution|Source Code Distribution]] on fetching source code and building instructions.

** The source code has been optimized to prepare for incoming new meta-analysis method in next ** Fixed bug estimating kinshipX with female samples.

*After downloading the source code, unzip and untar it, and cd polymutt2, and then type Make ...rated by vcf2map (the vcf file can be a complete vcf with all variants and samples)

| File containing haplotype data for target (gwas) samples. Must be a VCF file. ...er estimates read from a M3VCF file will be further updated using the gwas samples. Will be ignored if VCF reference file. [Default: OFF]

...make sure RAREMETALWORKER analyze chromosome X correctly, '''male must be code as 1 and female must be coded as 2''' in [[RAREMETALWORKER#PED_and_DAT_File * When samples are analyzed as unrelated (no any kind of kinship is used for linear mixed

...with that in .vcf file. The computation will be intensive if the number of samples are large.

key command: glfSplit<br>Source codes: ~goncalo/code/glfSplit/ == (5) Check total (aggregated over all individual samples) depth for each population, each platform ==

| File containing haplotype data for target (gwas) samples. Must be a VCF file. | This is number of samples to be stored in the memory before writing a VCF file piece

A source code package can be downloaded from [http://csg.sph.umich.edu//abecasis/download The pedigree file describes relationships among individuals and indicates samples for whom DNA is available (and who can thus be selected for sequencing) and

The following is an extract from the School of Public Health's Student Code of Conduct [http://www.sph.umich.edu/academics/policies/conduct.html]: ...net.'' '''44''':955-9. PMID: 22820512 [[Biostatistics 830 - Code Snippets|[Code Snippets]]]

immense help in making the code faster. -omosome X only male samples. Also added --rsid option to use

...ameter estimate; otherwise, a genetic map file for option <code>--mapFile</code> is required. ...is option is automatically ignored except when <code>--referenceEstimates</code> is OFF.

...the fifth nucleotide is encoded with the character "G". Its decimal ASCII code is 71, so the base quality of this nucleotide is 38 (71-33) [mpileup] 1 samples in 1 input files

All samples have some version of the Exome Chip or exome/whole genome sequences. Indiv For our first analysis, samples must be between ages 18 and 70 (inclusive) and be of European ancestry. We

User can compile the library without ZLIB, but then the code will not be able to read compressed files (typically BAM files are compress This will allow us to see where in the code it hit a segmentation fault. This method isn't perfect and may still leave

...strate how TrioCaller works in sequence data including trios and unrelated samples. We will walk through all necessary steps to move from raw sequence data to ...t a little descriptive information (e.g. Affiliation, depth, the number of samples and family structure). We will notify you if there is any update.&nbsp;

...iduals), and checks whether the reads are contaminated as a mixture of two samples. '''verifyBamID''' can detect sample contamination and swaps when external # Souce Code including libStatGen (uses a fixed version of libStatGen)

...specify the correct function for the -log10 uniform ourself. Here is some code which will do that with some sample data: [[Category:Code Samples]]

....1000genomes.org 1000 Genomes Project]. As with other 1000 Genomes Project samples, these individuals have been sequenced to an average depth of about 4x. ...d in fastq file. For this workshop, you will find DNA sequence reads for 3 samples in fastq format. To conserve disk space, the files have been compressed wit

The following is an extract from the School of Public Health's Student Code of Conduct [http://www.sph.umich.edu/academics/policies/conduct.html]: ...net.'' '''44''':955-9. PMID: 22820512 [[Biostatistics 830 - Code Snippets|[Code Snippets]]]

v0.17 fixed a bug when some of the samples in the per files are not in the input vcf file ...s also desirable to use more families or mixture of families and unrelated samples for polymutt.

...ipts to use <code>/usr/bin/env perl</code> instead of <code>/usr/bin/perl</code> to make it compatible with more users * Update default aligner to <code>bwa mem</code>

...able options. Or you could try to issue the command <code>MARKERLABEL SNP</code> to indicate that marker names are tabulated in a column labelled '''SNP''' ...of writing <code>MARKERLABEL SNP</code>, you could write <code>MARKER SNP</code>. If you make a mistake and METAL doesn't understand your command, it will

.../samtools/Makefile</code> and <code>gotcloud/src/samtools-hybrid/Makefile</code> :*#: <code>-D_CURSES_LIB=1</code>

...du/cfuchsb/minimac2.2014.9.15.src.tgz from here]. For compiling the source code, you need a recent [https://gcc.gnu.org gcc] (>=4.8), [http://www.openblas. Minimac2 comes in two flavours, <code>minimac2</code> and <code>minimac2-omp</code>. The latter version uses the [[OpenMP]] protocol to support multi-threadin

We have tested compilation using our source code on several platforms including Linux, and Mac OS X. For source code and executables together with instructions of building from source, please

...titative trait.<br />For binary trait, the recommended way of coding is to code controls as 1, cases as 2, missing phenotypes as -9 or 0. ...ation tests on CFH and ARMS2 genes. If there is no providing <code>--gene</code> option, all genes will be tests.

...file (tar xvf), cd into the libStatGen directory and type <code>make all</code>. **** Add subset samples parameter to ReadRecord

...requires external software packages to be copied to <code>UMAKE_HOME/ext/</code> directory ...projects/samtools/files/tabix/ TABIX Download] (after compiling the source code, copy bgzip and tabix to the "ext" folder above)

Here is the code used to create the image at the top of the page [[Category:Code Samples]]

...netic Variation-Methods and Protocols, Chapter 19, Humana Press 2010) with code available from http://sites.google.com/site/mikeweale/software/gwascode ...s. In a first pre-phasing step, haplotypes are estimated for all available samples. In a second step, missing alleles are imputed directly onto these phased h

** Fixed an error which occasionally report mismatches in the number of samples * '''NS''' : Number of phenotyped samples with non-missing genotypes

*NS&nbsp;: Number of samples with non-missing genotypes === 1. How do I code the INDEL variant names and alleles? ===

...sg.sph.umich.edu/cfuchsb/minimac-beta-2013.7.17.tgz from here] and source code [http://csg.sph.umich.edu/cfuchsb/minimac.src.tgz from here] ...minimac comes in two flavours, <code>minimac</code> and <code>minimac-omp</code>. The latter version uses the [[OpenMP]] protocol to support multi-threadin

For source code and executables together with instructions of building from source, please ...s are saved in DAT file. Note that you must specify <code>--makeResiduals</code> in order to adjust the covariates out of the phenotype. See [[RAREMETALWOR