Final PED documentation
This commit is contained in:
Mark DePristo
parent
3226d5dc0d
commit
be2d29ce69
|
|
@ -213,55 +213,63 @@ public class GATKArgumentCollection {
|
|||
// --------------------------------------------------------------------------------------------------------------
|
||||
|
||||
/**
|
||||
* Reads PED file-formatted tabular text files describing meta-data about the samples being
|
||||
* processed in the GATK.
|
||||
* <p>Reads PED file-formatted tabular text files describing meta-data about the samples being
|
||||
* processed in the GATK.</p>
|
||||
*
|
||||
* See http://www.broadinstitute.org/mpg/tagger/faq.html
|
||||
* See http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped
|
||||
* <ul>
|
||||
* <li>see <a href="http://www.broadinstitute.org/mpg/tagger/faq.html">http://www.broadinstitute.org/mpg/tagger/faq.html</a></li>
|
||||
* <li>see <a href="http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped">http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped</a></li>
|
||||
* </ul>
|
||||
*
|
||||
* The PED file is a white-space (space or tab) delimited file: the first six columns are mandatory:
|
||||
* <p>The PED file is a white-space (space or tab) delimited file: the first six columns are mandatory:</p>
|
||||
*
|
||||
* Family ID
|
||||
* Individual ID
|
||||
* Paternal ID
|
||||
* Maternal ID
|
||||
* Sex (1=male; 2=female; other=unknown)
|
||||
* Phenotype
|
||||
* <ul>
|
||||
* <li>Family ID</li>
|
||||
* <li>Individual ID</li>
|
||||
* <li>Paternal ID</li>
|
||||
* <li>Maternal ID</li>
|
||||
* <li>Sex (1=male; 2=female; other=unknown)</li>
|
||||
* <li>Phenotype</li>
|
||||
* </ul>
|
||||
*
|
||||
* The IDs are alphanumeric: the combination of family and individual ID should uniquely identify a person.
|
||||
* <p>The IDs are alphanumeric: the combination of family and individual ID should uniquely identify a person.
|
||||
* A PED file must have 1 and only 1 phenotype in the sixth column. The phenotype can be either a
|
||||
* quantitative trait or an affection status column: GATK will automatically detect which type
|
||||
* (i.e. based on whether a value other than 0, 1, 2 or the missing genotype code is observed).
|
||||
* (i.e. based on whether a value other than 0, 1, 2 or the missing genotype code is observed).</p>
|
||||
*
|
||||
* If an individual's sex is unknown, then any character other than 1 or 2 can be used.
|
||||
* <p>If an individual's sex is unknown, then any character other than 1 or 2 can be used.</p>
|
||||
*
|
||||
* You can add a comment to a PED or MAP file by starting the line with a # character. The rest of that
|
||||
* line will be ignored. Do not start any family IDs with this character therefore.
|
||||
* <p>You can add a comment to a PED or MAP file by starting the line with a # character. The rest of that
|
||||
* line will be ignored. Do not start any family IDs with this character therefore.</p>
|
||||
*
|
||||
* Affection status should be coded:
|
||||
* <p>Affection status should be coded:</p>
|
||||
*
|
||||
* -9 missing
|
||||
* 0 missing
|
||||
* 1 unaffected
|
||||
* 2 affected
|
||||
* <ul>
|
||||
* <li>-9 missing</li>
|
||||
* <li>0 missing</li>
|
||||
* <li>1 unaffected</li>
|
||||
* <li>2 affected</li>
|
||||
* </ul>
|
||||
*
|
||||
* If any value outside of -9,0,1,2 is detected than the samples are assumed
|
||||
* <p>If any value outside of -9,0,1,2 is detected than the samples are assumed
|
||||
* to phenotype values are interpreted as string phenotype values. In this case -9 uniquely
|
||||
* represents the missing value.
|
||||
* represents the missing value.</p>
|
||||
*
|
||||
* Genotypes (column 7 onwards) cannot be specified to the GATK.
|
||||
* <p>Genotypes (column 7 onwards) cannot be specified to the GATK.</p>
|
||||
*
|
||||
* For example, here are two individuals (one row = one person):
|
||||
* <p>For example, here are two individuals (one row = one person):</p>
|
||||
*
|
||||
* <pre>
|
||||
* FAM001 1 0 0 1 2
|
||||
* FAM001 2 0 0 1 2
|
||||
* </pre>
|
||||
*
|
||||
* Each -ped argument can be tagged with NO_FAMILY_ID, NO_PARENTS, NO_SEX, NO_PHENOTYPE to
|
||||
* tell the GATK PED parser that the corresponding fields are missing from the ped file.
|
||||
* <p>Each -ped argument can be tagged with NO_FAMILY_ID, NO_PARENTS, NO_SEX, NO_PHENOTYPE to
|
||||
* tell the GATK PED parser that the corresponding fields are missing from the ped file.</p>
|
||||
*
|
||||
* Note that most GATK walkers do not use pedigree information. Walkers that require pedigree
|
||||
* <p>Note that most GATK walkers do not use pedigree information. Walkers that require pedigree
|
||||
* data should clearly indicate so in their arguments and will throw errors if required pedigree
|
||||
* information is missing.
|
||||
* information is missing.</p>
|
||||
*/
|
||||
@Argument(fullName="pedigree", shortName = "ped", doc="Pedigree files for samples",required=false)
|
||||
public List<File> pedigreeFiles = Collections.emptyList();
|
||||
|
|
|
|||
|
|
@ -28,6 +28,14 @@ package org.broadinstitute.sting.gatk.samples;
|
|||
*
|
||||
*/
|
||||
public enum PedigreeValidationType {
|
||||
/**
|
||||
* Require if a pedigree file is provided at all samples in the VCF or BAM files have a corresponding
|
||||
* entry in the pedigree file(s).
|
||||
*/
|
||||
STRICT,
|
||||
|
||||
/**
|
||||
* Do not enforce any overlap between the VCF/BAM samples and the pedigree data
|
||||
* */
|
||||
SILENT
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue