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| <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' | ||
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||
| # 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> | ||
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| include::header.inc[] | ||
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| Plugin setGT | ||
| ------------ | ||
|
|
||
| The plugin `+setGT` allows to edit genotypes | ||
|
|
||
| The list of plugin-specific options can be obtained by running | ||
| `bcftools +setGT -h`, which will print the following usage page: | ||
| ---- | ||
| 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' | ||
| ---- | ||
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| include::footer.inc[] | ||
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