Skip to content

Commit

Permalink
Fix the QUAL calculation at REF-only sites and the use of AFs obtaine…
Browse files Browse the repository at this point in the history 
…d from QS in haploid calling

Also remove the QS(ref)=epsilon hack, which is probably not necessary.
  • Loading branch information
@pd3
pd3 committed Jan 19, 2017
1 parent 26745ca commit 7c56870
Show file tree
Hide file tree
Showing 4 changed files with 51 additions and 40 deletions.
51 changes: 31 additions & 20 deletions mcall.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -601,7 +601,6 @@ static int mcall_find_best_alleles(call_t *call, int nals, int *out_als)
if ( *pdg ) { lk_tot += log(*pdg); lk_tot_set = 1; }
pdg += ngts;
}

if ( ia==0 ) ref_lk = lk_tot; // likelihood of 0/0 for all samples
else lk_tot += call->theta; // the prior
UPDATE_MAX_LKs(1<<ia, ia>0 && lk_tot_set);
Expand All @@ -621,14 +620,16 @@ static int mcall_find_best_alleles(call_t *call, int nals, int *out_als)
int lk_tot_set = 0;
double fa = call->qsum[ia]/(call->qsum[ia]+call->qsum[ib]);
double fb = call->qsum[ib]/(call->qsum[ia]+call->qsum[ib]);
double fab = 2*fa*fb; fa *= fa; fb *= fb;
double fa2 = fa*fa;
double fb2 = fb*fb;
double fab = 2*fa*fb;
int isample, ibb = (ib+1)*(ib+2)/2-1, iab = iaa - ia + ib;
double *pdg = call->pdg;
for (isample=0; isample<nsmpl; isample++)
{
double val = 0;
if ( !call->ploidy || call->ploidy[isample]==2 )
val = fa*pdg[iaa] + fb*pdg[ibb] + fab*pdg[iab];
val = fa2*pdg[iaa] + fb2*pdg[ibb] + fab*pdg[iab];
else if ( call->ploidy && call->ploidy[isample]==1 )
val = fa*pdg[iaa] + fb*pdg[ibb];
if ( val ) { lk_tot += log(val); lk_tot_set = 1; }
Expand Down Expand Up @@ -661,15 +662,18 @@ static int mcall_find_best_alleles(call_t *call, int nals, int *out_als)
double fa = call->qsum[ia]/(call->qsum[ia]+call->qsum[ib]+call->qsum[ic]);
double fb = call->qsum[ib]/(call->qsum[ia]+call->qsum[ib]+call->qsum[ic]);
double fc = call->qsum[ic]/(call->qsum[ia]+call->qsum[ib]+call->qsum[ic]);
double fab = 2*fa*fb, fac = 2*fa*fc, fbc = 2*fb*fc; fa *= fa; fb *= fb; fc *= fc;
double fa2 = fa*fa;
double fb2 = fb*fb;
double fc2 = fc*fc;
double fab = 2*fa*fb, fac = 2*fa*fc, fbc = 2*fb*fc;
int isample, icc = (ic+1)*(ic+2)/2-1;
int iac = iaa - ia + ic, ibc = ibb - ib + ic;
double *pdg = call->pdg;
for (isample=0; isample<nsmpl; isample++)
{
double val = 0;
if ( !call->ploidy || call->ploidy[isample]==2 )
val = fa*pdg[iaa] + fb*pdg[ibb] + fc*pdg[icc] + fab*pdg[iab] + fac*pdg[iac] + fbc*pdg[ibc];
val = fa2*pdg[iaa] + fb2*pdg[ibb] + fc2*pdg[icc] + fab*pdg[iab] + fac*pdg[iac] + fbc*pdg[ibc];
else if ( call->ploidy && call->ploidy[isample]==1 )
val = fa*pdg[iaa] + fb*pdg[ibb] + fc*pdg[icc];
if ( val ) { lk_tot += log(val); lk_tot_set = 1; }
Expand Down Expand Up @@ -789,7 +793,7 @@ static void mcall_call_genotypes(call_t *call, bcf1_t *rec, int nals, int nout_a
{
if ( !(out_als & 1<<ia) ) continue; // ia-th allele not in the final selection, skip
int iaa = (ia+1)*(ia+2)/2-1; // PL index of the ia/ia genotype
double lk = pdg[iaa]*call->qsum[ia]*call->qsum[ia];
double lk = ploidy==2 ? pdg[iaa]*call->qsum[ia]*call->qsum[ia] : pdg[iaa]*call->qsum[ia];
#if USE_PRIOR_FOR_GTS
if ( ia!=0 ) lk *= prior;
#endif
Expand Down Expand Up @@ -943,7 +947,7 @@ static void mcall_call_trio_genotypes(call_t *call, bcf1_t *rec, int nals, int n
if ( !(out_als & 1<<ia) ) continue; // ia-th allele not in the final selection, skip
int iaa = bcf_alleles2gt(ia,ia); // PL index of the ia/ia genotype
int idx = bcf_alleles2gt(call->als_map[ia],call->als_map[ia]);
double lk = pdg[iaa]*call->qsum[ia]*call->qsum[ia];
double lk = ploidy==2 ? pdg[iaa]*call->qsum[ia]*call->qsum[ia] : pdg[iaa]*call->qsum[ia];
sum_lk += lk;
gls[idx] = lk;
if ( best_lk < lk )
Expand Down Expand Up @@ -1436,18 +1440,22 @@ int mcall(call_t *call, bcf1_t *rec)

float qsum_tot = 0;
for (i=0; i<nals; i++) qsum_tot += call->qsum[i];
if ( !call->qsum[0] )
{
// As P(RR)!=0 even for QS(ref)=0, we set QS(ref) to a small value,
// an equivalent of a single reference read.
if ( bcf_get_info_int32(call->hdr, rec, "DP", &call->itmp, &call->n_itmp)!=1 )
error("Could not read DP at %s:%d\n", call->hdr->id[BCF_DT_CTG][rec->rid].key,rec->pos+1);
if ( call->itmp[0] )
{
call->qsum[0] = 1.0 / call->itmp[0] / nsmpl;
qsum_tot += call->qsum[0];
}
}

// Is this still necessary??
//
// if (0&& !call->qsum[0] )
// {
// // As P(RR)!=0 even for QS(ref)=0, we set QS(ref) to a small value,
// // an equivalent of a single reference read.
// if ( bcf_get_info_int32(call->hdr, rec, "DP", &call->itmp, &call->n_itmp)!=1 )
// error("Could not read DP at %s:%d\n", call->hdr->id[BCF_DT_CTG][rec->rid].key,rec->pos+1);
// if ( call->itmp[0] )
// {
// call->qsum[0] = 1.0 / call->itmp[0] / nsmpl;
// qsum_tot += call->qsum[0];
// }
// }

if ( qsum_tot ) for (i=0; i<nals; i++) call->qsum[i] /= qsum_tot;
#endif

Expand Down Expand Up @@ -1532,7 +1540,10 @@ int mcall(call_t *call, bcf1_t *rec)
else
{
// Set the quality of a REF site
rec->qual = -4.343*(call->lk_sum - logsumexp2(call->lk_sum,call->ref_lk));
if ( call->lk_sum==-HUGE_VAL ) // no support from (high quality) reads, so QUAL=1-prior
rec->qual = call->theta ? -4.343*call->theta : 0;
else
rec->qual = -4.343*(call->lk_sum - logsumexp2(call->lk_sum,call->ref_lk));
}

if ( rec->qual>999 ) rec->qual = 999;
Expand Down
22 changes: 11 additions & 11 deletions test/mpileup.X.2.out
View file
Original file line number Diff line number Diff line change
Expand Up @@ -27,14 +27,14 @@
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00100 HG00101 HG00102
X 302 . T TA 481 . INDEL;IDV=7;IMF=1;DP=25;VDB=0.27613;SGB=-4.22417;MQSB=0.0443614;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=2,4,8,11;MQ=49 GT:PL:DP:DV 0/1:167,0,96:11:6 1:157,9:7:6 1/1:201,21,0:7:7
X 828 . T C 321 . DP=25;VDB=0.842082;SGB=-4.20907;RPB=0.950652;MQB=1;MQSB=1;BQB=0.929717;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=2,4,8,11;MQ=60 GT:PL:DP:DV 0/1:211,0,35:12:10 1:116,91:9:5 1/1:120,12,0:4:4
X 834 . G A 308 . DP=25;VDB=0.788006;SGB=-4.01214;RPB=0.999233;MQB=1;MQSB=1;BQB=0.821668;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=2,3,7,10;MQ=60 GT:PL:DP:DV 0/1:185,0,46:11:9 1:128,59:8:5 1/1:89,9,0:3:3
X 1665 . T C 3.10525 . DP=20;VDB=0.1;SGB=0.346553;RPB=0.222222;MQB=0.611111;MQSB=0.988166;BQB=0.944444;MQ0F=0;ICB=0.235294;HOB=0.18;AC=1;AN=5;DP4=7,11,1,1;MQ=55 GT:PL:DP:DV 0/0:0,21,185:7:0 0:0,222:9:0 0/1:35,0,51:4:2
X 1869 . A T 119 . DP=24;VDB=0.928022;SGB=-11.9537;RPB=0.984127;MQB=0.96464;MQSB=0.931547;BQB=0.359155;MQ0F=0;ICB=0.461538;HOB=0.02;AC=3;AN=5;DP4=6,9,5,4;MQ=58 GT:PL:DP:DV 0/1:115,0,224:18:7 0:16,104:5:1 1/1:42,3,0:1:1
X 2041 . G A 424 . DP=31;VDB=0.816435;SGB=-4.18892;RPB=0.88473;MQB=0.972375;MQSB=0.968257;BQB=0.311275;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=6,5,12,7;MQ=58 GT:PL:DP:DV 0/1:229,0,212:21:11 1:32,24:2:1 1/1:223,21,0:7:7
X 2220 . G A 257 . DP=21;VDB=0.532753;SGB=-3.51597;RPB=0.964198;MQB=0.898397;MQSB=0.875769;BQB=0.0354359;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=6,2,1,11;MQ=58 GT:PL:DP:DV 0/1:139,0,130:12:6 1:69,46:4:2 1/1:131,12,0:4:4
X 2564 . A G 178 . DP=15;VDB=0.690812;SGB=-3.20711;RPB=0.197899;MQB=1;MQSB=1;BQB=0.965069;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=1,4,4,5;MQ=60 GT:PL:DP:DV 0/1:88,0,78:6:3 1:57,56:4:2 1/1:124,12,0:4:4
X 3104 . C T 24.1975 . DP=25;VDB=0.8;SGB=0.346553;RPB=0.717391;MQB=0.956522;MQSB=0.962269;BQB=0.978261;MQ0F=0;ICB=0.235294;HOB=0.18;AC=1;AN=5;DP4=8,15,2,0;MQ=58 GT:PL:DP:DV 0/0:0,48,255:16:0 0:0,144:4:0 0/1:59,0,93:5:2
X 3587 . G A 332 . DP=29;VDB=0.902044;SGB=-3.91326;RPB=0.800999;MQB=1;MQSB=1;BQB=0.156944;MQ0F=0;ICB=0.461538;HOB=0.02;AC=3;AN=5;DP4=4,7,10,6;MQ=60 GT:PL:DP:DV 0/1:161,0,184:14:7 0:22,118:5:1 1/1:212,24,0:8:8
X 3936 . A G 412 . DP=37;VDB=0.0574114;SGB=-4.60123;RPB=0.741697;MQB=0.812605;MQSB=0.143788;BQB=0.883831;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=5,6,6,17;MQ=56 GT:PL:DP:DV 0/1:233,0,206:20:11 1:77,58:6:4 1/1:196,24,0:8:8
X 302 . T TA 482 . INDEL;IDV=7;IMF=1;DP=25;VDB=0.27613;SGB=-4.22417;MQSB=0.0443614;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=2,4,8,11;MQ=49 GT:PL:DP:DV 0/1:167,0,96:11:6 1:157,9:7:6 1/1:201,21,0:7:7
X 828 . T C 322 . DP=25;VDB=0.842082;SGB=-4.20907;RPB=0.950652;MQB=1;MQSB=1;BQB=0.929717;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=2,4,8,11;MQ=60 GT:PL:DP:DV 0/1:211,0,35:12:10 1:116,91:9:5 1/1:120,12,0:4:4
X 834 . G A 309 . DP=25;VDB=0.788006;SGB=-4.01214;RPB=0.999233;MQB=1;MQSB=1;BQB=0.821668;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=2,3,7,10;MQ=60 GT:PL:DP:DV 0/1:185,0,46:11:9 1:128,59:8:5 1/1:89,9,0:3:3
X 1665 . T C 3.44176 . DP=20;VDB=0.1;SGB=0.346553;RPB=0.222222;MQB=0.611111;MQSB=0.988166;BQB=0.944444;MQ0F=0;ICB=0.235294;HOB=0.18;AC=1;AN=5;DP4=7,11,1,1;MQ=55 GT:PL:DP:DV 0/0:0,21,185:7:0 0:0,222:9:0 0/1:35,0,51:4:2
X 1869 . A T 122 . DP=24;VDB=0.928022;SGB=-11.9537;RPB=0.984127;MQB=0.96464;MQSB=0.931547;BQB=0.359155;MQ0F=0;ICB=0.461538;HOB=0.02;AC=3;AN=5;DP4=6,9,5,4;MQ=58 GT:PL:DP:DV 0/1:115,0,224:18:7 0:16,104:5:1 1/1:42,3,0:1:1
X 2041 . G A 426 . DP=31;VDB=0.816435;SGB=-4.18892;RPB=0.88473;MQB=0.972375;MQSB=0.968257;BQB=0.311275;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=6,5,12,7;MQ=58 GT:PL:DP:DV 0/1:229,0,212:21:11 1:32,24:2:1 1/1:223,21,0:7:7
X 2220 . G A 259 . DP=21;VDB=0.532753;SGB=-3.51597;RPB=0.964198;MQB=0.898397;MQSB=0.875769;BQB=0.0354359;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=6,2,1,11;MQ=58 GT:PL:DP:DV 0/1:139,0,130:12:6 1:69,46:4:2 1/1:131,12,0:4:4
X 2564 . A G 180 . DP=15;VDB=0.690812;SGB=-3.20711;RPB=0.197899;MQB=1;MQSB=1;BQB=0.965069;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=1,4,4,5;MQ=60 GT:PL:DP:DV 0/1:88,0,78:6:3 1:57,56:4:2 1/1:124,12,0:4:4
X 3104 . C T 24.8375 . DP=25;VDB=0.8;SGB=0.346553;RPB=0.717391;MQB=0.956522;MQSB=0.962269;BQB=0.978261;MQ0F=0;ICB=0.235294;HOB=0.18;AC=1;AN=5;DP4=8,15,2,0;MQ=58 GT:PL:DP:DV 0/0:0,48,255:16:0 0:0,144:4:0 0/1:59,0,93:5:2
X 3587 . G A 335 . DP=29;VDB=0.902044;SGB=-3.91326;RPB=0.800999;MQB=1;MQSB=1;BQB=0.156944;MQ0F=0;ICB=0.461538;HOB=0.02;AC=3;AN=5;DP4=4,7,10,6;MQ=60 GT:PL:DP:DV 0/1:161,0,184:14:7 0:22,118:5:1 1/1:212,24,0:8:8
X 3936 . A G 414 . DP=37;VDB=0.0574114;SGB=-4.60123;RPB=0.741697;MQB=0.812605;MQSB=0.143788;BQB=0.883831;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=5,6,6,17;MQ=56 GT:PL:DP:DV 0/1:233,0,206:20:11 1:77,58:6:4 1/1:196,24,0:8:8
12 changes: 6 additions & 6 deletions test/mpileup.X.out
View file
Original file line number Diff line number Diff line change
Expand Up @@ -27,14 +27,14 @@
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00100 HG00101 HG00102
X 302 . T TA 481 . INDEL;IDV=7;IMF=1;DP=25;VDB=0.27613;SGB=-4.22417;MQSB=0.0443614;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=2,4,8,11;MQ=49 GT:PL:DP:DV 0/1:167,0,96:11:6 1:157,9:7:6 1/1:201,21,0:7:7
X 828 . T C 321 . DP=25;VDB=0.842082;SGB=-4.20907;RPB=0.950652;MQB=1;MQSB=1;BQB=0.929717;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=2,4,8,11;MQ=60 GT:PL:DP:DV 0/1:211,0,35:12:10 1:116,91:9:5 1/1:120,12,0:4:4
X 834 . G A 308 . DP=25;VDB=0.788006;SGB=-4.01214;RPB=0.999233;MQB=1;MQSB=1;BQB=0.821668;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=2,3,7,10;MQ=60 GT:PL:DP:DV 0/1:185,0,46:11:9 1:128,59:8:5 1/1:89,9,0:3:3
X 302 . T TA 482 . INDEL;IDV=7;IMF=1;DP=25;VDB=0.27613;SGB=-4.22417;MQSB=0.0443614;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=2,4,8,11;MQ=49 GT:PL:DP:DV 0/1:167,0,96:11:6 1:157,9:7:6 1/1:201,21,0:7:7
X 828 . T C 322 . DP=25;VDB=0.842082;SGB=-4.20907;RPB=0.950652;MQB=1;MQSB=1;BQB=0.929717;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=2,4,8,11;MQ=60 GT:PL:DP:DV 0/1:211,0,35:12:10 1:116,91:9:5 1/1:120,12,0:4:4
X 834 . G A 309 . DP=25;VDB=0.788006;SGB=-4.01214;RPB=0.999233;MQB=1;MQSB=1;BQB=0.821668;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=2,3,7,10;MQ=60 GT:PL:DP:DV 0/1:185,0,46:11:9 1:128,59:8:5 1/1:89,9,0:3:3
X 1665 . T C 3.10665 . DP=20;VDB=0.1;SGB=0.346553;RPB=0.222222;MQB=0.611111;MQSB=0.988166;BQB=0.944444;MQ0F=0;ICB=0.128205;HOB=0.0555556;AC=1;AN=6;DP4=7,11,1,1;MQ=55 GT:PL:DP:DV 0/0:0,21,185:7:0 0/0:0,27,222:9:0 0/1:35,0,51:4:2
X 1869 . A T 138 . DP=24;VDB=0.928022;SGB=-11.9537;RPB=0.984127;MQB=0.96464;MQSB=0.931547;BQB=0.359155;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=6,9,5,4;MQ=58 GT:PL:DP:DV 0/1:115,0,224:18:7 0/1:16,0,104:5:1 1/1:42,3,0:1:1
X 2041 . G A 447 . DP=31;VDB=0.816435;SGB=-4.18892;RPB=0.88473;MQB=0.972375;MQSB=0.968257;BQB=0.311275;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=6,5,12,7;MQ=58 GT:PL:DP:DV 0/1:229,0,212:21:11 0/1:32,0,24:2:1 1/1:223,21,0:7:7
X 2220 . G A 303 . DP=21;VDB=0.532753;SGB=-3.51597;RPB=0.964198;MQB=0.898397;MQSB=0.875769;BQB=0.0354359;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=6,2,1,11;MQ=58 GT:PL:DP:DV 0/1:139,0,130:12:6 0/1:69,0,46:4:2 1/1:131,12,0:4:4
X 2564 . A G 233 . DP=15;VDB=0.690812;SGB=-3.20711;RPB=0.197899;MQB=1;MQSB=1;BQB=0.965069;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=1,4,4,5;MQ=60 GT:PL:DP:DV 0/1:88,0,78:6:3 0/1:57,0,56:4:2 1/1:124,12,0:4:4
X 3104 . C T 24.1975 . DP=25;VDB=0.8;SGB=0.346553;RPB=0.717391;MQB=0.956522;MQSB=0.962269;BQB=0.978261;MQ0F=0;ICB=0.235294;HOB=0.18;AC=1;AN=5;DP4=8,15,2,0;MQ=58 GT:PL:DP:DV 0/0:0,48,255:16:0 0:0,144:4:0 0/1:59,0,93:5:2
X 3587 . G A 332 . DP=29;VDB=0.902044;SGB=-3.91326;RPB=0.800999;MQB=1;MQSB=1;BQB=0.156944;MQ0F=0;ICB=0.461538;HOB=0.02;AC=3;AN=5;DP4=4,7,10,6;MQ=60 GT:PL:DP:DV 0/1:161,0,184:14:7 0:22,118:5:1 1/1:212,24,0:8:8
X 3936 . A G 412 . DP=37;VDB=0.0574114;SGB=-4.60123;RPB=0.741697;MQB=0.812605;MQSB=0.143788;BQB=0.883831;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=5,6,6,17;MQ=56 GT:PL:DP:DV 0/1:233,0,206:20:11 1:77,58:6:4 1/1:196,24,0:8:8
X 3104 . C T 24.8375 . DP=25;VDB=0.8;SGB=0.346553;RPB=0.717391;MQB=0.956522;MQSB=0.962269;BQB=0.978261;MQ0F=0;ICB=0.235294;HOB=0.18;AC=1;AN=5;DP4=8,15,2,0;MQ=58 GT:PL:DP:DV 0/0:0,48,255:16:0 0:0,144:4:0 0/1:59,0,93:5:2
X 3587 . G A 335 . DP=29;VDB=0.902044;SGB=-3.91326;RPB=0.800999;MQB=1;MQSB=1;BQB=0.156944;MQ0F=0;ICB=0.461538;HOB=0.02;AC=3;AN=5;DP4=4,7,10,6;MQ=60 GT:PL:DP:DV 0/1:161,0,184:14:7 0:22,118:5:1 1/1:212,24,0:8:8
X 3936 . A G 414 . DP=37;VDB=0.0574114;SGB=-4.60123;RPB=0.741697;MQB=0.812605;MQSB=0.143788;BQB=0.883831;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=5,6,6,17;MQ=56 GT:PL:DP:DV 0/1:233,0,206:20:11 1:77,58:6:4 1/1:196,24,0:8:8
6 changes: 3 additions & 3 deletions test/mpileup.cAls.out
View file
Original file line number Diff line number Diff line change
Expand Up @@ -29,10 +29,10 @@
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00100 HG00101 HG00102
17 1 . A G,T 52 . DP=11;MQ0F=0;AC=0,0;AN=0;DP4=11,0,0,0;MQ=29 GT:PL:DP:DV ./.:0,0,0,0,0,0:5:0 ./.:.:3:0 ./.:.:3:0
17 2 . A T,G 52 . DP=11;MQ0F=0;AC=0,0;AN=0;DP4=11,0,0,0;MQ=29 GT:PL:DP:DV ./.:0,0,0,0,0,0:5:0 ./.:.:3:0 ./.:.:3:0
17 3 . A C 999 . DP=11;MQ0F=0;AC=0;AN=0;DP4=11,0,0,0;MQ=29 GT:PL:DP:DV ./.:0,0,0:5:0 ./.:.:3:0 ./.:.:3:0
17 3 . A C 26.0007 . DP=11;MQ0F=0;AC=0;AN=0;DP4=11,0,0,0;MQ=29 GT:PL:DP:DV ./.:0,0,0:5:0 ./.:.:3:0 ./.:.:3:0
17 4 . A G,T,C 21.815 . DP=11;MQ0F=0;AC=0,0,0;AN=2;DP4=11,0,0,0;MQ=29 GT:PL:DP:DV 0/0:1,2,3,7,8,10,11,12,14,15:5:0 ./.:.:3:0 ./.:.:3:0
17 5 . A G,T 999 . DP=11;MQ0F=0;AC=0,0;AN=0;DP4=11,0,0,0;MQ=29 GT:PL:DP:DV ./.:0,0,0,0,0,0:5:0 ./.:.:3:0 ./.:.:3:0
17 6 . A T,G 999 . DP=11;MQ0F=0;AC=0,0;AN=0;DP4=11,0,0,0;MQ=29 GT:PL:DP:DV ./.:0,0,0,0,0,0:5:0 ./.:.:3:0 ./.:.:3:0
17 5 . A G,T 26.0007 . DP=11;MQ0F=0;AC=0,0;AN=0;DP4=11,0,0,0;MQ=29 GT:PL:DP:DV ./.:0,0,0,0,0,0:5:0 ./.:.:3:0 ./.:.:3:0
17 6 . A T,G 26.0007 . DP=11;MQ0F=0;AC=0,0;AN=0;DP4=11,0,0,0;MQ=29 GT:PL:DP:DV ./.:0,0,0,0,0,0:5:0 ./.:.:3:0 ./.:.:3:0
17 7 . A T,G,C 21.5769 . DP=11;MQ0F=0;AC=0,0,0;AN=2;DP4=11,0,0,0;MQ=29 GT:PL:DP:DV 0/0:1,2,3,4,5,6,2,3,5,3:5:0 ./.:.:3:0 ./.:.:3:0
17 828 . T C 409 . DP=25;VDB=0.842082;SGB=-4.20907;RPB=0.950652;MQB=1;MQSB=1;BQB=0.929717;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=2,4,8,11;MQ=60 GT:PL:DP:DV 0/1:211,0,35:12:10 0/1:116,0,91:9:5 1/1:120,12,0:4:4
17 1665 . T C 3.10665 . DP=20;VDB=0.1;SGB=0.346553;RPB=0.222222;MQB=0.611111;MQSB=0.988166;BQB=0.944444;MQ0F=0;ICB=0.128205;HOB=0.0555556;AC=1;AN=6;DP4=7,11,1,1;MQ=55 GT:PL:DP:DV 0/0:0,21,185:7:0 0/0:0,27,222:9:0 0/1:35,0,51:4:2
Expand Down

0 comments on commit 7c56870

Please sign in to comment.