zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge pull request #1571 from broadinstitute/rhl_vtbp_doc_1570 

Update PLINK link and change lines to columns
This commit is contained in:
Ron Levine 2017-03-23 14:22:05 -04:00 committed by GitHub
parent 485a090ef6 278985b8bd
commit 728b3db8e0
1 changed files with 3 additions and 3 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java
View File

@ -53,14 +53,14 @@ import java.util.*;
* Convert VCF to binary pedigree file
*
* <p>This tool takes a VCF and produces a binary pedigree as used by
* <a href="http://pngu.mgh.harvard.edu/~purcell/plink/">PLINK</a>, consisting of three associated files (.bed/.bim/.fam).</p>
* <a href="https://www.cog-genomics.org/plink">PLINK</a>, consisting of three associated files (.bed/.bim/.fam).</p>
*
* <h3>Inputs</h3>
* <p>
* A VCF file and a metadata file.
* </p>
*
* <p>The metaData file can take two formats, the first of which is the first 6 lines of the standard pedigree file. This
* <p>The metaData file can take two formats, the first of which is the first 6 columns of the standard pedigree file. This
* is what Plink describes as a .fam file. Note that the sex encoding convention is 1=male; 2=female; other=unknown. An example .fam file is as follows (note that there is no header):</p>
* <pre>
* CEUTrio NA12878 NA12891 NA12892 2 -9
@ -85,7 +85,7 @@ import java.util.*;
*
* <h3>Outputs</h3>
* <p>
* A binary pedigree in PLINK format, composed of three files (.bed/.bim/.fam). See the <a href='http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped'>PLINK format specification</a> for more details.
* A binary pedigree in PLINK format, composed of three files (.bed/.bim/.fam). See the <a href='https://www.cog-genomics.org/plink/2.0/formats'>PLINK format specification</a> for more details.
* </p>
*
* <h3>Example</h3>