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• EMADS Primary Analysis Plan
  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
  14 KB (2,173 words) - 23:03, 14 November 2013
• RAREMETAL FAQ
  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
  7 KB (1,054 words) - 11:46, 20 March 2018
• TrioCaller
  ...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. 
  15 KB (2,470 words) - 18:01, 19 May 2015
• VerifyBamID
  ...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)
  20 KB (2,795 words) - 15:29, 9 September 2017
• Code Sample: Generating QQ Plots in R
  ...specify the correct function for the -log10 uniform ourself. Here is some code which will do that with some sample data: [[Category:Code Samples]]
  9 KB (1,398 words) - 14:14, 12 November 2013
• Tutorial: Low Pass Sequence Analysis
  ....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
  18 KB (2,867 words) - 03:59, 17 September 2019
• Biostatistics 866: Main Page
  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]]]
  9 KB (1,319 words) - 07:21, 18 April 2017
• Polymutt
  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.
  13 KB (2,106 words) - 10:12, 27 April 2014
• GotCloud: Versions
  ...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>
  18 KB (2,762 words) - 12:17, 14 May 2015
• METAL Quick Start
  ...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
  18 KB (2,804 words) - 13:11, 5 April 2010
• GotCloud: FAQs
  .../samtools/Makefile</code> and <code>gotcloud/src/samtools-hybrid/Makefile</code> :*#: <code>-D_CURSES_LIB=1</code>
  12 KB (1,871 words) - 10:54, 23 June 2015
• Minimac2
  ...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
  13 KB (2,050 words) - 12:53, 9 March 2018
• RAREMETAL Documentation
  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
  24 KB (3,256 words) - 13:22, 20 May 2019
• Rvtests
  ...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.
  29 KB (4,420 words) - 00:31, 12 May 2016
• LibStatGen Download
  ...file (tar xvf), cd into the libStatGen directory and type <code>make all</code>. **** Add subset samples parameter to ReadRecord
  10 KB (1,430 words) - 00:04, 13 November 2017
• UMAKE
  ...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)
  16 KB (2,060 words) - 11:53, 2 February 2017
• Code Sample: Generating Manhattan Plots in R
  Here is the code used to create the image at the top of the page [[Category:Code Samples]]
  19 KB (3,167 words) - 10:49, 14 January 2014
• IMPUTE2: 1000 Genomes Imputation Cookbook
  ...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
  13 KB (2,049 words) - 05:19, 11 September 2012
• EPACTS
  ** Fixed an error which occasionally report mismatches in the number of samples * '''NS''' : Number of phenotyped samples with non-missing genotypes
  41 KB (5,647 words) - 08:03, 19 February 2019
• EPACTS for DIAGRAM
  *NS&nbsp;: Number of samples with non-missing genotypes === 1. How do I code the INDEL variant names and alleles? ===
  24 KB (3,442 words) - 10:05, 2 February 2017

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