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Add support for inverting phase of genotypes with setGT plugin #2367

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Merged
merged 1 commit into from
Mar 5, 2025
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Merged

Add support for inverting phase of genotypes with setGT plugin #2367

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24 changes: 24 additions & 0 deletions plugins/setGT.c
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Original file line number Diff line number Diff line change
Expand Up @@ -82,6 +82,7 @@ args_t *args = NULL;
#define GT_CUSTOM (1<<10)
#define GT_X_VAF (1<<11)
#define GT_RAND (1<<12)
#define GT_INVPHASE (1<<13)

#define MINOR_ALLELE -1
#define MAJOR_ALLELE -2
Expand Down Expand Up @@ -113,6 +114,7 @@ const char *usage(void)
" X .. allele with bigger read depth as determined from FMT/AD\n"
" p .. phase genotype (0/1 becomes 0|1)\n"
" u .. unphase genotype and sort by allele (1|0 becomes 0/1)\n"
" i .. invert the genotype phase (0|1 becomes 1|0)\n"
"Usage: bcftools +setGT [General Options] -- [Plugin Options]\n"
"Options:\n"
" run \"bcftools plugin\" for a list of common options\n"
Expand Down Expand Up @@ -235,6 +237,7 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
if ( strchr(optarg,'X') ) args->new_mask |= GT_X_VAF;
if ( strchr(optarg,'p') ) args->new_mask |= GT_PHASED;
if ( strchr(optarg,'u') ) args->new_mask |= GT_UNPHASED;
if ( strchr(optarg,'i') ) args->new_mask |= GT_INVPHASE;
if ( !strncmp(optarg,"c:",2) ) { args->new_mask |= GT_CUSTOM; args->custom.gt_str = optarg; }
if ( args->new_mask==0 ) error("Unknown parameter to --new-gt: %s\n", optarg);
break;
Expand Down Expand Up @@ -364,6 +367,21 @@ static inline int unphase_gt(int32_t *ptr, int ngts)
return changed;
}

// invert the phase for a single sample, ngts is the ploidy
static inline int invert_phase_gt(int32_t *ptr, int ngts)
{
int gt;
if ( ngts!=2 ) return 0; // don't invert the phase for sample ploidy != 2
if ( ptr[0]==bcf_int32_vector_end || ptr[1]==bcf_int32_vector_end ) return 0;
gt = bcf_gt_allele(ptr[1]);
if (bcf_gt_is_phased(ptr[1]))
ptr[1] = bcf_gt_phased(bcf_gt_allele(ptr[0]));
else
ptr[1] = bcf_gt_unphased(bcf_gt_allele(ptr[0]));
ptr[0] = bcf_gt_unphased(gt); // first gt doesn't carry the phased flag per BCF specifications
return 2;
}

// sets GT for a single sample, ngts is the ploidy, allele
static inline int set_gt(int32_t *ptr, int ngts, int allele)
{
Expand Down Expand Up @@ -543,6 +561,8 @@ bcf1_t *process(bcf1_t *rec)
}
else if ( args->new_mask & GT_X_VAF )
changed += set_gt(ptr, ngts, args->xarr[i]);
else if ( args->new_mask & GT_INVPHASE )
changed += invert_phase_gt(ptr, ngts);
else
changed += set_gt(ptr, ngts, args->new_gt);
}
Expand Down Expand Up @@ -584,6 +604,8 @@ bcf1_t *process(bcf1_t *rec)
}
else if ( args->new_mask & GT_X_VAF )
changed += set_gt(args->gts + i*ngts, ngts, args->xarr[i]);
else if ( args->new_mask & GT_INVPHASE )
changed += invert_phase_gt(args->gts, ngts);
else
changed += set_gt(args->gts + i*ngts, ngts, args->new_gt);
}
Expand Down Expand Up @@ -620,6 +642,8 @@ bcf1_t *process(bcf1_t *rec)
}
else if ( args->new_mask & GT_X_VAF )
changed += set_gt(ptr, ngts, args->xarr[i]);
else if ( args->new_mask & GT_INVPHASE )
changed += invert_phase_gt(ptr, ngts);
else
changed += set_gt(ptr, ngts, args->new_gt);
}
Expand Down
17 changes: 17 additions & 0 deletions test/setGT.2.1.out
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@@ -0,0 +1,17 @@
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##contig=<ID=20,length=81195210>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depth">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00100 HG00101 HG00102 HG00200 HG00201 HG00202
20 302 . T TA 999 . . GT:AD 1|0:55,5 0|1:55,5 1|1:5,55 1|0:55,5 0|1:55,5 1|1:5,55
20 828 . T C 999 . . GT:AD 1|0:55,5 1|1:55,5 1|1:5,55 1|0:55,5 0|1:55,5 1|1:5,55
20 834 . G A 999 . . GT:AD 1|0:55,5 1|0:55,5 1|1:5,55 0|1:55,5 0|1:55,5 1|1:5,55
20 1665 . T C 999 . . GT:AD 0|1:55,5 1|0:55,5 1|0:5,55 1|0:55,5 0|1:55,5 1|1:5,55
20 1869 . A T 999 . . GT:AD 1|0:55,5 0|0:55,5 1|1:5,55 1|0:55,5 0|1:55,5 1|1:5,55
20 2041 . G A 999 . . GT:AD 1|0:55,5 1|1:55,5 1|1:5,55 1|0:55,5 0|1:55,5 1|1:5,55
20 2220 . G A 999 . . GT:AD 1|0:55,5 0|1:55,5 1|1:5,55 1|0:55,5 0|1:55,5 1|1:5,55
20 2564 . A G 999 . . GT:AD 1|0:55,5 1|1:55,5 1|1:5,55 1|0:55,5 0|1:55,5 1|1:5,55
20 3104 . C T 999 . . GT:AD 0|0:5,5 0|0:5,5 1|0:5,5 1|0:5,5 0|1:5,5 1|1:5,5
20 3587 . G A 999 . . GT:AD 1|0:5,5 1|0:5,5 1|1:5,5 1|0:5,5 0|1:5,5 1|1:5,5
20 3936 . A G 999 . . GT:AD 1|0:1,2 1|1:3,4 1|1:5,6 1|0:7,8 0|1:9,1 1|1:2,3
1 change: 1 addition & 0 deletions test/test.pl
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Expand Up @@ -633,6 +633,7 @@
run_test(\&test_vcf_plugin,$opts,in=>'setGT',out=>'setGT.1.out',cmd=>'+setGT --no-version',args=>'-- -t q -n 0 -i \'GT~"." && FMT/DP=30 && GQ=150\'');
run_test(\&test_vcf_plugin,$opts,in=>'setGT.2',out=>'setGT.2.out',cmd=>'+setGT --no-version',args=>'-- -t q -n . -i \'GT[@{QPATH}/setGT.samples.txt]="het"\'');
run_test(\&test_vcf_plugin,$opts,in=>'setGT.2',out=>'setGT.3.out',cmd=>'+setGT --no-version',args=>'-- -t q -n . -i \'GT[@{QPATH}/setGT.samples.txt]="het" & binom(AD[@{QPATH}/setGT.samples.txt])<0.1\'');
run_test(\&test_vcf_plugin,$opts,in=>'setGT.2',out=>'setGT.2.1.out',cmd=>'+setGT --no-version',args=>'-- -t a -n i');
run_test(\&test_vcf_plugin,$opts,in=>'setGT.3',out=>'setGT.3.1.out',cmd=>'+setGT --no-version',args=>'-- -t a -n pM');
run_test(\&test_vcf_plugin,$opts,in=>'setGT.3',out=>'setGT.3.2.out',cmd=>'+setGT --no-version',args=>'-- -t a -n pm');
run_test(\&test_vcf_plugin,$opts,in=>'setGT.3',out=>'setGT.3.3.out',cmd=>'+setGT --no-version',args=>'-- -t a -n c:1');
Expand Down