From 278985b8bd4c22e0858c6d9377cc41fe6233c253 Mon Sep 17 00:00:00 2001 From: Ron Levine Date: Thu, 23 Mar 2017 11:46:38 -0400 Subject: [PATCH] Update PLINK link and change lines to columns --- .../tools/walkers/variantutils/VariantsToBinaryPed.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java index 57c0fe7ff..8ec77ff2b 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToBinaryPed.java @@ -53,14 +53,14 @@ import java.util.*; * Convert VCF to binary pedigree file * *

This tool takes a VCF and produces a binary pedigree as used by - * PLINK, consisting of three associated files (.bed/.bim/.fam).

+ * PLINK, consisting of three associated files (.bed/.bim/.fam).

* *

Inputs

*

* A VCF file and a metadata file. *

* -*

The metaData file can take two formats, the first of which is the first 6 lines of the standard pedigree file. This +*

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):

* 
  * CEUTrio NA12878 NA12891 NA12892 2 -9
@@ -85,7 +85,7 @@ import java.util.*;
  *
  * 
Outputs

  * 

- * A binary pedigree in PLINK format, composed of three files (.bed/.bim/.fam). See the PLINK format specification for more details.
+ * A binary pedigree in PLINK format, composed of three files (.bed/.bim/.fam). See the PLINK format specification for more details.
  * 

  *
  * 
Example