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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