extern double kf_gammap(double s, double z);
int test16(bcf1_t *b, anno16_t *a);
-int call_multiallelic_gt(bcf1_t *b, bcf_p1aux_t *ma, double threshold)
+// Wigginton 2005, PMID: 15789306
+// written by Jan Wigginton
+double calc_hwe(int obs_hom1, int obs_hom2, int obs_hets)
+{
+ if (obs_hom1 + obs_hom2 + obs_hets == 0 ) return 1;
+
+ assert(obs_hom1 >= 0 && obs_hom2 >= 0 && obs_hets >= 0);
+
+ int obs_homc = obs_hom1 < obs_hom2 ? obs_hom2 : obs_hom1;
+ int obs_homr = obs_hom1 < obs_hom2 ? obs_hom1 : obs_hom2;
+
+ int rare_copies = 2 * obs_homr + obs_hets;
+ int genotypes = obs_hets + obs_homc + obs_homr;
+
+ double *het_probs = (double*) calloc(rare_copies+1, sizeof(double));
+
+ /* start at midpoint */
+ int mid = rare_copies * (2 * genotypes - rare_copies) / (2 * genotypes);
+
+ /* check to ensure that midpoint and rare alleles have same parity */
+ if ((rare_copies & 1) ^ (mid & 1)) mid++;
+
+ int curr_hets = mid;
+ int curr_homr = (rare_copies - mid) / 2;
+ int curr_homc = genotypes - curr_hets - curr_homr;
+
+ het_probs[mid] = 1.0;
+ double sum = het_probs[mid];
+ for (curr_hets = mid; curr_hets > 1; curr_hets -= 2)
+ {
+ het_probs[curr_hets - 2] = het_probs[curr_hets] * curr_hets * (curr_hets - 1.0) / (4.0 * (curr_homr + 1.0) * (curr_homc + 1.0));
+ sum += het_probs[curr_hets - 2];
+
+ /* 2 fewer heterozygotes for next iteration -> add one rare, one common homozygote */
+ curr_homr++;
+ curr_homc++;
+ }
+
+ curr_hets = mid;
+ curr_homr = (rare_copies - mid) / 2;
+ curr_homc = genotypes - curr_hets - curr_homr;
+ for (curr_hets = mid; curr_hets <= rare_copies - 2; curr_hets += 2)
+ {
+ het_probs[curr_hets + 2] = het_probs[curr_hets] * 4.0 * curr_homr * curr_homc /((curr_hets + 2.0) * (curr_hets + 1.0));
+ sum += het_probs[curr_hets + 2];
+
+ /* add 2 heterozygotes for next iteration -> subtract one rare, one common homozygote */
+ curr_homr--;
+ curr_homc--;
+ }
+ int i;
+ for (i = 0; i <= rare_copies; i++) het_probs[i] /= sum;
+
+ /* p-value calculation for p_hwe */
+ double p_hwe = 0.0;
+ for (i = 0; i <= rare_copies; i++)
+ {
+ if (het_probs[i] > het_probs[obs_hets])
+ continue;
+ p_hwe += het_probs[i];
+ }
+
+ p_hwe = p_hwe > 1.0 ? 1.0 : p_hwe;
+ free(het_probs);
+ return p_hwe;
+
+}
+
+
+static void _bcf1_set_ref(bcf1_t *b, int idp)
+{
+ kstring_t s;
+ int old_n_gi = b->n_gi;
+ s.m = b->m_str; s.l = b->l_str - 1; s.s = b->str;
+ kputs(":GT", &s); kputc('\0', &s);
+ b->m_str = s.m; b->l_str = s.l; b->str = s.s;
+ bcf_sync(b);
+
+ // Call GTs
+ int isample, an = 0;
+ for (isample = 0; isample < b->n_smpl; isample++)
+ {
+ if ( idp>=0 && ((uint16_t*)b->gi[idp].data)[isample]==0 )
+ ((uint8_t*)b->gi[old_n_gi].data)[isample] = 1<<7;
+ else
+ {
+ ((uint8_t*)b->gi[old_n_gi].data)[isample] = 0;
+ an += b->ploidy ? b->ploidy[isample] : 2;
+ }
+ }
+ bcf_fit_alt(b,1);
+ b->qual = 999;
+
+ // Prepare BCF for output: ref, alt, filter, info, format
+ memset(&s, 0, sizeof(kstring_t)); kputc('\0', &s);
+ kputs(b->ref, &s); kputc('\0', &s);
+ kputs(b->alt, &s); kputc('\0', &s); kputc('\0', &s);
+ {
+ ksprintf(&s, "AN=%d;", an);
+ kputs(b->info, &s);
+ anno16_t a;
+ int has_I16 = test16(b, &a) >= 0? 1 : 0;
+ if (has_I16 )
+ {
+ if ( a.is_tested) ksprintf(&s, ";PV4=%.2g,%.2g,%.2g,%.2g", a.p[0], a.p[1], a.p[2], a.p[3]);
+ ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq);
+ }
+ kputc('\0', &s);
+ rm_info(&s, "I16=");
+ rm_info(&s, "QS=");
+ }
+ kputs(b->fmt, &s); kputc('\0', &s);
+ free(b->str);
+ b->m_str = s.m; b->l_str = s.l; b->str = s.s;
+ bcf_sync(b);
+}
+
+int call_multiallelic_gt(bcf1_t *b, bcf_p1aux_t *ma, double threshold, int var_only)
{
int nals = 1;
char *p;
}
if ( b->alt[0] && !*p ) nals++;
- if ( nals==1 ) return 1;
-
if ( nals>4 )
{
if ( *b->ref=='N' ) return 0;
exit(1);
}
- // find PL and DP FORMAT indexes
+ // find PL, DV and DP FORMAT indexes
uint8_t *pl = NULL;
- int npl = 0, idp=-1;
- int i;
+ int i, npl = 0, idp = -1, idv = -1;
for (i = 0; i < b->n_gi; ++i)
{
if (b->gi[i].fmt == bcf_str2int("PL", 2))
pl = (uint8_t*)b->gi[i].data;
npl = b->gi[i].len;
}
- if (b->gi[i].fmt == bcf_str2int("DP", 2)) idp=i;
+ else if (b->gi[i].fmt == bcf_str2int("DP", 2)) idp=i;
+ else if (b->gi[i].fmt == bcf_str2int("DV", 2)) idv=i;
+ }
+ if ( nals==1 )
+ {
+ if ( !var_only ) _bcf1_set_ref(b, idp);
+ return 1;
}
if ( !pl ) return -1;
if ( sscanf(p+3,"%lf,%lf,%lf,%lf",&qsum[0],&qsum[1],&qsum[2],&qsum[3])!=4 ) { fprintf(stderr,"Could not parse %s\n",p); exit(1); }
- // Calculate the most likely combination of alleles
+ // Calculate the most likely combination of alleles, remembering the most and second most likely set
int ia,ib,ic, max_als=0, max_als2=0;
- double ref_lk = 0, max_lk = INT_MIN, max_lk2 = INT_MIN, lk_sum = INT_MIN;
+ double ref_lk = 0, max_lk = INT_MIN, max_lk2 = INT_MIN, lk_sum = INT_MIN, lk_sums[3];
for (ia=0; ia<nals; ia++)
{
double lk_tot = 0;
else if ( max_lk2<lk_tot ) { max_lk2 = lk_tot; max_als2 = 1<<ia; }
lk_sum = lk_tot>lk_sum ? lk_tot + log(1+exp(lk_sum-lk_tot)) : lk_sum + log(1+exp(lk_tot-lk_sum));
}
+ lk_sums[0] = lk_sum;
if ( nals>1 )
{
for (ia=0; ia<nals; ia++)
lk_sum = lk_tot>lk_sum ? lk_tot + log(1+exp(lk_sum-lk_tot)) : lk_sum + log(1+exp(lk_tot-lk_sum));
}
}
+ lk_sums[1] = lk_sum;
}
if ( nals>2 )
{
}
}
}
+ lk_sums[2] = lk_sum;
}
// Should we add another allele, does it increase the likelihood significantly?
for (i=0; i<nals; i++) if ( max_als2&1<<i) n2++;
if ( n2<n1 && kf_gammap(1,2.0*(max_lk-max_lk2))<threshold )
{
- max_lk = max_lk2;
+ // the threshold not exceeded, use the second most likely set with fewer alleles
+ max_lk = max_lk2;
max_als = max_als2;
+ n1 = n2;
}
+ lk_sum = lk_sums[n1-1];
// Get the BCF record ready for GT and GQ
kstring_t s;
// Call GTs
int isample, gts=0, ac[4] = {0,0,0,0};
+ int nRR = 0, nAA = 0, nRA = 0, max_dv = 0, dp_nref = 0;
for (isample = 0; isample < b->n_smpl; isample++)
{
int ploidy = b->ploidy ? b->ploidy[isample] : 2;
double *p = pdg + isample*npdg;
int ia, als = 0;
- double lk = 0, lk_sum=0;
+ double lk = 0, lk_s = 0;
for (ia=0; ia<nals; ia++)
{
if ( !(max_als&1<<ia) ) continue;
int iaa = (ia+1)*(ia+2)/2-1;
double _lk = p[iaa]*qsum[ia]*qsum[ia];
if ( _lk > lk ) { lk = _lk; als = ia<<3 | ia; }
- lk_sum += _lk;
+ lk_s += _lk;
}
if ( ploidy==2 )
{
int iab = iaa - ia + ib;
double _lk = 2*qsum[ia]*qsum[ib]*p[iab];
if ( _lk > lk ) { lk = _lk; als = ib<<3 | ia; }
- lk_sum += _lk;
+ lk_s += _lk;
}
}
}
- lk = -log(1-lk/lk_sum)/0.2302585;
- if ( idp>=0 && ((uint16_t*)b->gi[idp].data)[isample]==0 )
+ lk = -log(1-lk/lk_s)/0.2302585;
+ int dp = 0;
+ if ( idp>=0 && (dp=((uint16_t*)b->gi[idp].data)[isample])==0 )
{
+ // no coverage
((uint8_t*)b->gi[old_n_gi].data)[isample] = 1<<7;
((uint8_t*)b->gi[old_n_gi+1].data)[isample] = 0;
continue;
}
+ if ( lk>99 ) lk = 99;
((uint8_t*)b->gi[old_n_gi].data)[isample] = als;
- ((uint8_t*)b->gi[old_n_gi+1].data)[isample] = lk<100 ? (int)lk : 99;
+ ((uint8_t*)b->gi[old_n_gi+1].data)[isample] = (int)lk;
+
+ // For MDV annotation
+ int dv;
+ if ( als && idv>=0 && (dv=((uint16_t*)b->gi[idv].data)[isample]) )
+ {
+ if ( max_dv < dv ) max_dv = dv;
+ dp_nref += dp;
+ }
+
+ // For HWE annotation; multiple ALT alleles treated as one
+ if ( !als ) nRR++;
+ else if ( !(als>>3&7) || !(als&7) ) nRA++;
+ else nAA++;
gts |= 1<<(als>>3&7) | 1<<(als&7);
ac[ als>>3&7 ]++;
ac[ als&7 ]++;
}
+ free(pdg);
bcf_fit_alt(b,max_als);
+ // The VCF spec is ambiguous about QUAL: is it the probability of anything else
+ // (that is QUAL(non-ref) = P(ref)+P(any non-ref other than ALT)) or is it
+ // QUAL(non-ref)=P(ref) and QUAL(ref)=1-P(ref)? Assuming the latter.
+ b->qual = gts>1 ? -4.343*(ref_lk - lk_sum) : -4.343*log(1-exp(ref_lk - lk_sum));
+ if ( b->qual>999 ) b->qual = 999;
// Prepare BCF for output: ref, alt, filter, info, format
memset(&s, 0, sizeof(kstring_t)); kputc('\0', &s);
{
if ( a.is_tested) ksprintf(&s, ";PV4=%.2g,%.2g,%.2g,%.2g", a.p[0], a.p[1], a.p[2], a.p[3]);
ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq);
+ ksprintf(&s, ";QBD=%e", b->qual/(a.d[0] + a.d[1] + a.d[2] + a.d[3]));
+ if ( dp_nref ) ksprintf(&s, ";QBDNR=%e", b->qual/dp_nref);
+ if ( max_dv ) ksprintf(&s, ";MDV=%d", max_dv);
+ }
+ if ( nAA+nRA )
+ {
+ double hwe = calc_hwe(nAA, nRR, nRA);
+ ksprintf(&s, ";HWE=%e", hwe);
}
kputc('\0', &s);
rm_info(&s, "I16=");
kputs(b->fmt, &s); kputc('\0', &s);
free(b->str);
b->m_str = s.m; b->l_str = s.l; b->str = s.s;
- b->qual = gts>1 ? -4.343*(ref_lk - lk_sum) : -4.343*(max_lk - lk_sum);
- if ( b->qual>999 ) b->qual = 999;
bcf_sync(b);
-
- free(pdg);
return gts;
}
projects / samtools.git / blobdiff