-
Notifications
You must be signed in to change notification settings - Fork 242
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
19 changed files
with
1,212 additions
and
329 deletions.
There are no files selected for viewing
Large diffs are not rendered by default.
Oops, something went wrong.
Large diffs are not rendered by default.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,157 @@ | ||
| <!DOCTYPE html> | ||
| <html lang="en"> | ||
| <head> | ||
| <meta charset="UTF-8"> | ||
| <meta http-equiv="X-UA-Compatible" content="IE=edge"> | ||
| <meta name="viewport" content="width=device-width, initial-scale=1.0"> | ||
| <meta name="generator" content="Asciidoctor 2.0.15.dev"> | ||
| <title>Plugin setGT</title> | ||
| <link rel="stylesheet" href="./index.css"> | ||
| </head> | ||
| <body class="article"> | ||
| <div id="header"> | ||
| </div> | ||
| <div id="content"> | ||
| <div class="sidebarblock navig"> | ||
| <div class="content"> | ||
| <div class="ulist"> | ||
| <div class="title">General</div> | ||
| <ul> | ||
| <li> | ||
| <p><a href="index.html">Main page</a></p> | ||
| </li> | ||
| <li> | ||
| <p><a href="../bcftools.html">Manual page</a></p> | ||
| </li> | ||
| <li> | ||
| <p><a href="install.html">Installation</a></p> | ||
| </li> | ||
| <li> | ||
| <p><a href="publications.html">Publications</a></p> | ||
| </li> | ||
| </ul> | ||
| </div> | ||
| <div class="ulist"> | ||
| <div class="title">Calling</div> | ||
| <ul> | ||
| <li> | ||
| <p><a href="cnv-calling.html">CNV calling</a></p> | ||
| </li> | ||
| <li> | ||
| <p><a href="csq-calling.html">Consequence calling</a></p> | ||
| </li> | ||
| <li> | ||
| <p><a href="consensus-sequence.html">Consensus calling</a></p> | ||
| </li> | ||
| <li> | ||
| <p><a href="roh-calling.html">ROH calling</a></p> | ||
| </li> | ||
| <li> | ||
| <p><a href="variant-calling.html">Variant calling and filtering</a></p> | ||
| </li> | ||
| </ul> | ||
| </div> | ||
| <div class="ulist"> | ||
| <div class="title">Tips and Tricks</div> | ||
| <ul> | ||
| <li> | ||
| <p><a href="convert.html">Converting formats</a></p> | ||
| </li> | ||
| <li> | ||
| <p><a href="annotate.html">Adding annotation</a></p> | ||
| </li> | ||
| <li> | ||
| <p><a href="query.html">Extracting information</a></p> | ||
| </li> | ||
| <li> | ||
| <p><a href="filtering.html">Filtering expressions</a></p> | ||
| </li> | ||
| <li> | ||
| <p><a href="scaling.html">Performance and Scaling</a></p> | ||
| </li> | ||
| <li> | ||
| <p><a href="plugins.html">Plugins</a></p> | ||
| </li> | ||
| <li> | ||
| <p><a href="FAQ.html">FAQ</a></p> | ||
| </li> | ||
| </ul> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| <div id="main"> | ||
| <div class="sect1"> | ||
| <h2 id="_plugin_setgt">Plugin setGT</h2> | ||
| <div class="sectionbody"> | ||
| <div class="paragraph"> | ||
| <p>The plugin <code>+setGT</code> allows to edit genotypes</p> | ||
| </div> | ||
| <div class="paragraph"> | ||
| <p>The list of plugin-specific options can be obtained by running | ||
| <code>bcftools +setGT -h</code>, which will print the following usage page:</p> | ||
| </div> | ||
| <div class="listingblock"> | ||
| <div class="content"> | ||
| <pre>About: Sets genotypes. The target genotypes can be specified as: | ||
| ./. .. completely missing ("." or "./.", depending on ploidy) | ||
| ./x .. partially missing (e.g., "./0" or ".|1" but not "./.") | ||
| . .. partially or completely missing | ||
| a .. all genotypes | ||
| b .. heterozygous genotypes failing two-tailed binomial test (example below) | ||
| q .. select genotypes using -i/-e options | ||
| r:FLOAT .. select randomly a proportion of FLOAT genotypes (can be combined with other modes) | ||
| and the new genotype can be one of: | ||
| . .. missing ("." or "./.", keeps ploidy) | ||
| 0 .. reference allele (e.g. 0/0 or 0, keeps ploidy) | ||
| c:GT .. custom genotype (e.g. 0/0, 0, 0/1, m/M, 0/X overrides ploidy) | ||
| m .. minor (the second most common) allele as determined from INFO/AC or FMT/GT (e.g. 1/1 or 1, keeps ploidy) | ||
| M .. major allele as determined from INFO/AC or FMT/GT (e.g. 1/1 or 1, keeps ploidy) | ||
| X .. allele with bigger read depth as determined from FMT/AD | ||
| p .. phase genotype (0/1 becomes 0|1) | ||
| u .. unphase genotype and sort by allele (1|0 becomes 0/1) | ||
| Usage: bcftools +setGT [General Options] -- [Plugin Options] | ||
| Options: | ||
| run "bcftools plugin" for a list of common options | ||
|
|
||
| Plugin options: | ||
| -e, --exclude EXPR Exclude a genotype if true (requires -t q) | ||
| -i, --include EXPR include a genotype if true (requires -t q) | ||
| -n, --new-gt TYPE Genotypes to set, see above | ||
| -s, --seed INT Random seed to use with -t r [0] | ||
| -t, --target-gt TYPE Genotypes to change, see above | ||
|
|
||
| Example: | ||
| # set missing genotypes ("./.") to phased ref genotypes ("0|0") | ||
| bcftools +setGT in.vcf -- -t . -n 0p | ||
|
|
||
| # set missing genotypes with DP>0 and GQ>20 to ref genotypes ("0/0") | ||
| bcftools +setGT in.vcf -- -t q -n 0 -i 'GT="." && FMT/DP>0 && GQ>20' | ||
|
|
||
| # set partially missing genotypes to completely missing | ||
| bcftools +setGT in.vcf -- -t ./x -n . | ||
|
|
||
| # set heterozygous genotypes to 0/0 if binom.test(nAlt,nRef+nAlt,0.5)<1e-3 | ||
| bcftools +setGT in.vcf -- -t "b:AD<1e-3" -n 0 | ||
|
|
||
| # force unphased heterozygous genotype if binom.test(nAlt,nRef+nAlt,0.5)>0.1 | ||
| bcftools +setGT in.vcf -- -t ./x -n c:'m/M'</pre> | ||
| </div> | ||
| </div> | ||
| <div class="sect2"> | ||
| <h3 id="_feedback">Feedback</h3> | ||
| <div class="paragraph"> | ||
| <p>We welcome your feedback, please help us improve this page by | ||
| either opening an <a href="https://github.com/samtools/bcftools/issues">issue on github</a> or <a href="https://github.com/samtools/bcftools/tree/gh-pages/howtos">editing it directly</a> and sending | ||
| a pull request.</p> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| <div id="footer"> | ||
| <div id="footer-text"> | ||
| </div> | ||
| </div> | ||
| </body> | ||
| </html> |
Oops, something went wrong.