Further improve the indel calling.

jkbonfield · jkbonfield · commit 16834c7ff96c · 2022-03-17T16:15:50.000Z
- We erroneously had the -m and -F pre-filter options applies as needing
  either to pass instead of both to pass in bcf_cgp_find_types.  Fixing
  this is a significant reduction to FP rates.

- The computation of which STRs spanned the indel being assessed was
  sometimes a little bit out, due to using "qpos" instead of "pos".
  This removes a few false negatives.

- Improve the calculation of indel cost ("iscore") by counting the
  number of additional repeat units beyond the end of the sequence.
  The old penalty for STRs at the end of reads has been removed,
  meaning we regain some FNs while still penalising (more) the cases
  that lead to FPs.

  Overall there is some small FP / FN adjustments, but the biggest
  improvement here is a significant drop in GT errors (~10% fewer).
diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
@@ -281,10 +281,10 @@ static int *bcf_cgp_find_types(int n, int *n_plp, bam_pileup1_t **plp,
                 break;
 
         if (sz == 0
-            || j-i >= bca->min_support
-            // Note, doesn't handle bca->per_sample_flt yet
-            || bca->per_sample_flt
-            || (double)(j-i) / n_tot >= bca->min_frac)
+            || (j-i >= bca->min_support &&
+                // Note, doesn't handle bca->per_sample_flt yet
+                (bca->per_sample_flt
+                 || (double)(j-i) / n_tot >= bca->min_frac)))
             types[t++] = sz;
         i = j-1;
     }
@@ -519,7 +519,8 @@ static char **bcf_cgp_consensus(int n, int *n_plp, bam_pileup1_t **plp,
                         // secondary consensus produced with the other
                         // deletion.  We set a marker for how long to
                         // skip adding to ref_base.
-                        skip_to = x+len;
+                        if (x > skip_to)
+                            skip_to = x+len;
                     }
                 }
                 break;
@@ -952,7 +953,7 @@ static int bcf_cgp_align_score(bam_pileup1_t *p, bcf_callaux_t *bca,
                                int tbeg, int tend1, int tend2,
                                int left, int right,
                                int qbeg, int qend,
-                               int qpos, int max_deletion,
+                               int pos, int qpos, int max_deletion,
                                int *score) {
     // Illumina
     probaln_par_t apf = { 1e-4, 1e-2, 10 };
@@ -1091,12 +1092,21 @@ static int bcf_cgp_align_score(bam_pileup1_t *p, bcf_callaux_t *bca,
     // This is emphasised further if the sequence ends with
     // soft clipping.
     DL_FOREACH_SAFE(reps, elt, tmp) {
-        if (elt->start <= qpos && elt->end >= qpos) {
-            iscore += (elt->end-elt->start) / elt->rep_len;  // c
-            if (elt->start+tbeg <= r_start ||
-                elt->end+tbeg   >= r_end) {
-                iscore += (elt->end-elt->start);
-            }
+        int str_beg = elt->start+tbeg;
+        int str_end = elt->end+tbeg;
+
+
+        if (str_beg <= pos && str_end >= pos) {
+            // Overlaps indel region; num repeat units.
+            iscore += (elt->end-elt->start) / elt->rep_len;
+        }
+#define STR_HALO2 (2+2*elt->rep_len)
+        if (str_beg <= pos+STR_HALO2 && str_end >= pos-STR_HALO2) {
+            // Worst: extends beyond read end by >= 1 repeat unit
+            if (str_beg <= r_start-elt->rep_len)
+                iscore += 10*(r_start - str_beg)/elt->rep_len;
+            if (str_end >= r_end+elt->rep_len)
+                iscore += 10*(elt->end+tbeg - r_end)/elt->rep_len;
        }
 
         DL_DELETE(reps, elt);
@@ -1505,7 +1515,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos,
                                             r_start, r_end, long_read,
                                             tbeg, tend1, tend2,
                                             left2, left + tcon_len[0],
-                                            qbeg, qend, qpos, -biggest_del,
+                                            qbeg, qend, pos,qpos, -biggest_del,
                                             &score[K*n_types + t]) < 0) {
                         goto err;
                     }
diff --git a/test/mpileup/indel-AD.1.out b/test/mpileup/indel-AD.1.out
@@ -166,9 +166,9 @@
 000000F	535	.	G	A,<*>	0	.	DP=125;I16=65,52,0,1,4309,171791,12,144,7020,421200,60,3600,2679,64385,25,625;QS=0.997223,0.00277713,0;SGB=-0.379885;RPBZ=-1.14518;MQBZ=0;MQSBZ=0;BQBZ=-1.74874;SCBZ=0.0762539;FS=0;MQ0F=0	PL:AD	0,255,255,255,255,255:117,1,0
 000000F	536	.	T	G,A,<*>	0	.	DP=125;I16=65,51,0,2,4274,171298,24,288,6960,417600,120,7200,2661,64041,48,1154;QS=0.994416,0.002792,0.002792,0;VDB=0.1;SGB=-0.453602;RPBZ=-1.69957;MQBZ=0;MQSBZ=0;BQBZ=-2.39373;SCBZ=-0.714873;FS=0;MQ0F=0	PL:AD	0,255,255,255,255,255,255,255,255,255:116,1,1,0
 000000F	537	.	A	<*>	0	.	DP=125;I16=65,53,0,0,4390,175290,0,0,7080,424800,0,0,2713,65375,0,0;QS=1,0;MQSBZ=0;FS=0;MQ0F=0	PL:AD	0,255,255:118,0
-000000F	537	.	AC	A	0	.	INDEL;IDV=60;IMF=0.48;DP=125;I16=37,25,31,27,2480,99200,2320,92800,3720,223200,3480,208800,1399,33485,1313,31375;QS=0.386704,0.613296;VDB=0.0486419;SGB=-0.693147;RPBZ=-0.543708;MQBZ=0;MQSBZ=0;SCBZ=0.641853;FS=0;MQ0F=0	PL:AD	255,0,193:62,58
+000000F	537	.	AC	A	0	.	INDEL;IDV=60;IMF=0.48;DP=125;I16=36,26,31,27,2480,99200,2320,92800,3720,223200,3480,208800,1405,33737,1313,31375;QS=0.385658,0.614342;VDB=0.0342923;SGB=-0.693147;RPBZ=-0.543708;MQBZ=0;MQSBZ=0;SCBZ=0.641853;FS=0;MQ0F=0	PL:AD	255,0,193:62,58
 000000F	538	.	C	<*>	0	.	DP=65;I16=36,26,0,0,2195,86349,0,0,3720,223200,0,0,1432,34600,0,0;QS=1,0;MQSBZ=0;FS=0;MQ0F=0	PL:AD	0,187,255:62,0
-000000F	538	.	CT	C	0	.	INDEL;IDV=64;IMF=0.512;DP=125;I16=31,27,37,26,2320,92800,2520,100800,3480,208800,3780,226800,1318,31556,1422,34128;QS=0.360065,0.639935;VDB=0.0467386;SGB=-0.693147;RPBZ=0.242079;MQBZ=0;MQSBZ=0;SCBZ=-0.994262;FS=0;MQ0F=0	PL:AD	255,0,195:58,62
+000000F	538	.	CT	C	0	.	INDEL;IDV=64;IMF=0.512;DP=125;I16=31,27,36,26,2320,92800,2480,99200,3480,208800,3720,223200,1318,31556,1405,33839;QS=0.360065,0.639935;VDB=0.0289027;SGB=-0.693147;RPBZ=0.242079;MQBZ=0;MQSBZ=0;SCBZ=-0.994262;FS=0;MQ0F=0	PL:AD	255,0,195:58,62
 000000F	539	.	T	<*>	0	.	DP=60;I16=29,26,0,0,2120,86238,0,0,3300,198000,0,0,1260,30374,0,0;QS=1,0;MQSBZ=0;FS=0;MQ0F=0	PL:AD	0,166,255:55,0
 000000F	540	.	G	<*>	0	.	DP=124;I16=64,53,0,0,4130,161310,0,0,7020,421200,0,0,2703,65511,0,0;QS=1,0;MQSBZ=0;FS=0;MQ0F=0	PL:AD	0,255,255:117,0
 000000F	541	.	G	<*>	0	.	DP=124;I16=64,53,0,0,4143,160525,0,0,7020,421200,0,0,2705,65703,0,0;QS=1,0;MQSBZ=0;FS=0;MQ0F=0	PL:AD	0,255,255:117,0
@@ -290,7 +290,7 @@
 000000F	656	.	A	<*>	0	.	DP=11;I16=4,7,0,0,404,15690,0,0,660,39600,0,0,141,2411,0,0;QS=1,0;MQSBZ=0;FS=0;MQ0F=0	PL:AD	0,33,255:11,0
 000000F	657	.	C	<*>	0	.	DP=11;I16=4,7,0,0,413,15607,0,0,660,39600,0,0,131,2189,0,0;QS=1,0;MQSBZ=0;FS=0;MQ0F=0	PL:AD	0,33,255:11,0
 000000F	658	.	A	<*>	0	.	DP=10;I16=3,7,0,0,121,1651,0,0,600,36000,0,0,122,1986,0,0;QS=1,0;MQSBZ=0;FS=0;MQ0F=0	PL:AD	0,30,79:10,0
-000000F	658	.	AA	AAATTA	0	.	INDEL;IDV=2;IMF=0.125;DP=16;I16=2,1,1,2,300,30000,300,30000,180,10800,180,10800,59,1205,50,902;QS=0.227273,0.772727;VDB=0.00155977;SGB=-0.511536;RPBZ=-1.70026;MQBZ=0;MQSBZ=0;SCBZ=-1.35678;FS=0;MQ0F=0	PL:AD	51,0,3:3,2
+000000F	658	.	AA	AAATTA	0	.	INDEL;IDV=2;IMF=0.125;DP=16;I16=2,1,3,2,300,30000,500,50000,180,10800,300,18000,59,1205,76,1240;QS=0.111111,0.888889;VDB=0.000108203;SGB=-0.590765;RPBZ=-1.70026;MQBZ=0;MQSBZ=0;SCBZ=-1.35678;FS=0;MQ0F=0	PL:AD	124,1,0:3,5
 000000F	659	.	A	<*>	0	.	DP=10;I16=3,5,0,0,86,1088,0,0,480,28800,0,0,75,1077,0,0;QS=1,0;MQSBZ=0;FS=0;MQ0F=0	PL:AD	0,24,63:8,0
 000000F	660	.	T	<*>	0	.	DP=2;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;FS=0;MQ0F=0	PL:AD	0,0,0:0,0
 000000F	661	.	A	<*>	0	.	DP=8;I16=0,2,0,0,8,32,0,0,120,7200,0,0,26,340,0,0;QS=1,0;FS=0;MQ0F=0	PL:AD	0,6,7:2,0
diff --git a/test/mpileup/indel-AD.2.out b/test/mpileup/indel-AD.2.out
@@ -21,4 +21,4 @@
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths (high-quality bases)">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample
 11	75	.	G	<*>	0	.	DP=68;I16=6,62,0,0,2437,87909,0,0,3770,217210,0,0,838,15940,0,0;QS=1,0;MQSBZ=0.140975;FS=0;MQ0F=0	PL:AD	0,205,255:68,0
-11	75	.	GTAAAATAAAATAAAATAAAATAAA	GTAAAATAAAATAAAATAAAATAAAATAAA	0	.	INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,9,1,5,1680,201600,720,86400,840,50400,174,5046,244,5778,147,3609;QS=0.730233,0.269767;VDB=0.00674908;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0.140975;SCBZ=-0.546919;FS=0;MQ0F=0	PL:AD	83,0,244:14,6
+11	75	.	GTAAAATAAAATAAAATAAAATAAA	GTAAAATAAAATAAAATAAAATAAAATAAA	0	.	INDEL;IDV=6;IMF=0.0882353;DP=68;I16=4,8,1,5,1440,172800,720,86400,720,43200,174,5046,244,5778,147,3609;QS=0.702055,0.297945;VDB=0.001602;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0.140975;SCBZ=-0.546919;FS=0;MQ0F=0	PL:AD	88,0,221:12,6
diff --git a/test/mpileup/indel-AD.3.out b/test/mpileup/indel-AD.3.out
@@ -21,4 +21,4 @@
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths (high-quality bases)">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample
 11	75	.	G	<*>	0	.	DP=68;I16=6,62,0,0,2437,87909,0,0,3770,217210,0,0,838,15940,0,0;QS=1,0;MQSBZ=0.140975;FS=0;MQ0F=0	PL:AD	0,205,255:68,0
-11	75	.	GTAAAATAAAATAAAATAAAATAAA	GTAAAATAAAATAAAATAAAATAAAATAAA	0	.	INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,9,1,5,1680,201600,720,86400,840,50400,174,5046,244,5778,147,3609;QS=0.730233,0.269767;VDB=0.00674908;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0.140975;SCBZ=-0.546919;FS=0;MQ0F=0	PL:AD	83,0,244:45,23
+11	75	.	GTAAAATAAAATAAAATAAAATAAA	GTAAAATAAAATAAAATAAAATAAAATAAA	0	.	INDEL;IDV=6;IMF=0.0882353;DP=68;I16=4,8,1,5,1440,172800,720,86400,720,43200,174,5046,244,5778,147,3609;QS=0.702055,0.297945;VDB=0.001602;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0.140975;SCBZ=-0.546919;FS=0;MQ0F=0	PL:AD	88,0,221:43,25
diff --git a/test/mpileup/indel-AD.4.out b/test/mpileup/indel-AD.4.out
@@ -21,4 +21,4 @@
 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths (high-quality bases)">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample
 11	75	.	G	<*>	0	.	DP=68;I16=6,62,0,0,2437,87909,0,0,3770,217210,0,0,838,15940,0,0;QS=1,0;MQSBZ=0.140975;FS=0;MQ0F=0	PL:AD	0,205,255:68,0
-11	75	.	GTAAAATAAAATAAAATAAAATAAA	GTAAAATAAAATAAAATAAAATAAAATAAA	0	.	INDEL;IDV=6;IMF=0.0882353;DP=68;I16=5,9,1,5,1680,201600,720,86400,840,50400,174,5046,244,5778,147,3609;QS=0.730233,0.269767;VDB=0.00674908;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0.140975;SCBZ=-0.546919;FS=0;MQ0F=0	PL:AD	83,0,244:62,6
+11	75	.	GTAAAATAAAATAAAATAAAATAAA	GTAAAATAAAATAAAATAAAATAAAATAAA	0	.	INDEL;IDV=6;IMF=0.0882353;DP=68;I16=4,8,1,5,1440,172800,720,86400,720,43200,174,5046,244,5778,147,3609;QS=0.702055,0.297945;VDB=0.001602;SGB=-0.616816;RPBZ=-3.24592;MQBZ=-6.13241;MQSBZ=0.140975;SCBZ=-0.546919;FS=0;MQ0F=0	PL:AD	88,0,221:62,6
diff --git a/test/mpileup/mpileup.2.out b/test/mpileup/mpileup.2.out
@@ -224,7 +224,7 @@
 17	300	.	A	<*>	0	.	DP=27;I16=11,15,0,0,1001,39455,0,0,1258,66538,0,0,469,10437,0,0;QS=3,0;MQSBZ=-3.34898;FS=0;MQ0F=0	PL:DP:DV	0,33,255:11:0	0,24,204:8:0	0,21,210:7:0
 17	301	.	G	<*>	0	.	DP=25;I16=10,14,0,0,928,36116,0,0,1169,62097,0,0,476,10632,0,0;QS=3,0;MQSBZ=-3.10529;FS=0;MQ0F=0	PL:DP:DV	0,30,255:10:0	0,21,195:7:0	0,21,196:7:0
 17	302	.	T	<*>	0	.	DP=25;I16=10,14,0,0,879,32885,0,0,1169,62097,0,0,483,10849,0,0;QS=3,0;MQSBZ=-3.10529;FS=0;MQ0F=0	PL:DP:DV	0,30,231:10:0	0,21,172:7:0	0,21,202:7:0
-17	302	.	T	TA	0	.	INDEL;IDV=7;IMF=1;DP=25;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.515744,2.48426;VDB=0.27613;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.10529;SCBZ=-0.268121;FS=0;MQ0F=0	PL:DP:DV	167,0,95:11:6	158,0,11:7:6	201,21,0:7:7
+17	302	.	T	TA	0	.	INDEL;IDV=7;IMF=1;DP=25;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.543141,2.45686;VDB=0.27613;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.10529;SCBZ=-0.268121;FS=0;MQ0F=0	PL:DP:DV	157,0,98:11:6	158,0,14:7:6	201,21,0:7:7
 17	303	.	G	<*>	0	.	DP=25;I16=10,15,0,0,968,37972,0,0,1229,65697,0,0,497,11181,0,0;QS=3,0;MQSBZ=-2.97044;FS=0;MQ0F=0	PL:DP:DV	0,33,255:11:0	0,21,197:7:0	0,21,195:7:0
 17	304	.	C	<*>	0	.	DP=27;I16=11,16,0,0,991,37005,0,0,1318,70138,0,0,503,11359,0,0;QS=3,0;MQSBZ=-2.39388;FS=0;MQ0F=0	PL:DP:DV	0,33,255:11:0	0,24,206:8:0	0,24,200:8:0
 17	305	.	C	<*>	0	.	DP=27;I16=11,16,0,0,1057,41761,0,0,1318,70138,0,0,510,11508,0,0;QS=3,0;MQSBZ=-2.39388;FS=0;MQ0F=0	PL:DP:DV	0,33,255:11:0	0,24,213:8:0	0,24,211:8:0
diff --git a/test/mpileup/mpileup.4.out b/test/mpileup/mpileup.4.out
@@ -228,7 +228,7 @@
 17	300	.	A	<*>	0	.	DP=27;DPR=26,0;I16=11,15,0,0,1001,39455,0,0,1258,66538,0,0,469,10437,0,0;QS=3,0;MQSBZ=-3.34898;FS=0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,33,255:11:0:0:6,5,0,0:11,0	0,24,204:8:0:0:3,5,0,0:8,0	0,21,210:7:0:0:2,5,0,0:7,0
 17	301	.	G	<*>	0	.	DP=25;DPR=24,0;I16=10,14,0,0,928,36116,0,0,1169,62097,0,0,476,10632,0,0;QS=3,0;MQSBZ=-3.10529;FS=0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,30,255:10:0:0:5,5,0,0:10,0	0,21,195:7:0:0:3,4,0,0:7,0	0,21,196:7:0:0:2,5,0,0:7,0
 17	302	.	T	<*>	0	.	DP=25;DPR=24,0;I16=10,14,0,0,879,32885,0,0,1169,62097,0,0,483,10849,0,0;QS=3,0;MQSBZ=-3.10529;FS=0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,30,231:10:0:0:5,5,0,0:10,0	0,21,172:7:0:0:3,4,0,0:7,0	0,21,202:7:0:0:2,5,0,0:7,0
-17	302	.	T	TA	0	.	INDEL;IDV=7;IMF=1;DP=25;DPR=6,19;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.515744,2.48426;VDB=0.27613;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.10529;SCBZ=-0.268121;FS=0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	167,0,95:11:6:6:1,4,4,2:5,6	158,0,11:7:6:0:1,0,2,4:1,6	201,21,0:7:7:0:0,0,2,5:0,7
+17	302	.	T	TA	0	.	INDEL;IDV=7;IMF=1;DP=25;DPR=6,19;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.543141,2.45686;VDB=0.27613;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.10529;SCBZ=-0.268121;FS=0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	157,0,98:11:6:6:1,4,4,2:5,6	158,0,14:7:6:0:1,0,2,4:1,6	201,21,0:7:7:0:0,0,2,5:0,7
 17	303	.	G	<*>	0	.	DP=25;DPR=25,0;I16=10,15,0,0,968,37972,0,0,1229,65697,0,0,497,11181,0,0;QS=3,0;MQSBZ=-2.97044;FS=0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,33,255:11:0:0:5,6,0,0:11,0	0,21,197:7:0:0:3,4,0,0:7,0	0,21,195:7:0:0:2,5,0,0:7,0
 17	304	.	C	<*>	0	.	DP=27;DPR=27,0;I16=11,16,0,0,991,37005,0,0,1318,70138,0,0,503,11359,0,0;QS=3,0;MQSBZ=-2.39388;FS=0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,33,255:11:0:0:5,6,0,0:11,0	0,24,206:8:0:0:4,4,0,0:8,0	0,24,200:8:0:0:2,6,0,0:8,0
 17	305	.	C	<*>	0	.	DP=27;DPR=27,0;I16=11,16,0,0,1057,41761,0,0,1318,70138,0,0,510,11508,0,0;QS=3,0;MQSBZ=-2.39388;FS=0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,33,255:11:0:0:5,6,0,0:11,0	0,24,213:8:0:0:4,4,0,0:8,0	0,24,211:8:0:0:2,6,0,0:8,0
diff --git a/test/mpileup/mpileup.5.out b/test/mpileup/mpileup.5.out
@@ -230,7 +230,7 @@
 17	300	.	A	<*>	0	.	DP=27;ADF=11,0;ADR=15,0;AD=26,0;I16=11,15,0,0,1001,39455,0,0,1258,66538,0,0,469,10437,0,0;QS=3,0;MQSBZ=-3.34898;FS=0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,33,255:11:0:6,0:5,0:11,0	0,24,204:8:0:3,0:5,0:8,0	0,21,210:7:0:2,0:5,0:7,0
 17	301	.	G	<*>	0	.	DP=25;ADF=10,0;ADR=14,0;AD=24,0;I16=10,14,0,0,928,36116,0,0,1169,62097,0,0,476,10632,0,0;QS=3,0;MQSBZ=-3.10529;FS=0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,30,255:10:0:5,0:5,0:10,0	0,21,195:7:0:3,0:4,0:7,0	0,21,196:7:0:2,0:5,0:7,0
 17	302	.	T	<*>	0	.	DP=25;ADF=10,0;ADR=14,0;AD=24,0;I16=10,14,0,0,879,32885,0,0,1169,62097,0,0,483,10849,0,0;QS=3,0;MQSBZ=-3.10529;FS=0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,30,231:10:0:5,0:5,0:10,0	0,21,172:7:0:3,0:4,0:7,0	0,21,202:7:0:2,0:5,0:7,0
-17	302	.	T	TA	0	.	INDEL;IDV=7;IMF=1;DP=25;ADF=2,8;ADR=4,11;AD=6,19;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.515744,2.48426;VDB=0.27613;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.10529;SCBZ=-0.268121;FS=0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	167,0,95:11:6:1,4:4,2:5,6	158,0,11:7:0:1,2:0,4:1,6	201,21,0:7:0:0,2:0,5:0,7
+17	302	.	T	TA	0	.	INDEL;IDV=7;IMF=1;DP=25;ADF=2,8;ADR=4,11;AD=6,19;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.543141,2.45686;VDB=0.27613;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.10529;SCBZ=-0.268121;FS=0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	157,0,98:11:6:1,4:4,2:5,6	158,0,14:7:0:1,2:0,4:1,6	201,21,0:7:0:0,2:0,5:0,7
 17	303	.	G	<*>	0	.	DP=25;ADF=10,0;ADR=15,0;AD=25,0;I16=10,15,0,0,968,37972,0,0,1229,65697,0,0,497,11181,0,0;QS=3,0;MQSBZ=-2.97044;FS=0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,33,255:11:0:5,0:6,0:11,0	0,21,197:7:0:3,0:4,0:7,0	0,21,195:7:0:2,0:5,0:7,0
 17	304	.	C	<*>	0	.	DP=27;ADF=11,0;ADR=16,0;AD=27,0;I16=11,16,0,0,991,37005,0,0,1318,70138,0,0,503,11359,0,0;QS=3,0;MQSBZ=-2.39388;FS=0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,33,255:11:0:5,0:6,0:11,0	0,24,206:8:0:4,0:4,0:8,0	0,24,200:8:0:2,0:6,0:8,0
 17	305	.	C	<*>	0	.	DP=27;ADF=11,0;ADR=16,0;AD=27,0;I16=11,16,0,0,1057,41761,0,0,1318,70138,0,0,510,11508,0,0;QS=3,0;MQSBZ=-2.39388;FS=0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,33,255:11:0:5,0:6,0:11,0	0,24,213:8:0:4,0:4,0:8,0	0,24,211:8:0:2,0:6,0:8,0
diff --git a/test/mpileup/mpileup.6.out b/test/mpileup/mpileup.6.out
@@ -62,7 +62,7 @@
 17	283	.	C	<*>	.	.	END=296;MinDP=5;QS=3,0	PL:DP	0,33,240:11	0,18,119:6	0,15,122:5
 17	297	.	C	G,<*>	0	.	DP=25;I16=9,15,1,0,901,34305,4,16,1138,59338,60,3600,445,9901,10,100;QS=2.98261,0.0173913,0;SGB=-0.556633;RPBZ=-1.24856;MQBZ=0.806872;MQSBZ=-3.22749;BQBZ=-1.67542;SCBZ=-0.368383;FS=0;MQ0F=0	PL:DP:DV	0,33,255,33,255,255:11:0	0,15,168,21,171,168:8:1	0,18,161,18,161,161:6:0
 17	298	.	A	<*>	.	.	END=301;MinDP=7;QS=3,0	PL:DP	0,30,231:10	0,21,172:7	0,21,189:7
-17	302	.	T	TA	0	.	INDEL;IDV=7;IMF=1;DP=25;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.515744,2.48426;VDB=0.27613;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.10529;SCBZ=-0.268121;FS=0;MQ0F=0	PL:DP:DV	167,0,95:11:6	158,0,11:7:6	201,21,0:7:7
+17	302	.	T	TA	0	.	INDEL;IDV=7;IMF=1;DP=25;I16=2,4,8,11,240,9600,760,30400,236,10564,993,55133,109,2229,377,8629;QS=0.543141,2.45686;VDB=0.27613;SGB=-4.22417;RPBZ=1.11989;MQBZ=1.47646;MQSBZ=-3.10529;SCBZ=-0.268121;FS=0;MQ0F=0	PL:DP:DV	157,0,98:11:6	158,0,14:7:6	201,21,0:7:7
 17	303	.	G	<*>	.	.	END=334;MinDP=7;QS=3,0	PL:DP	0,30,235:10	0,21,197:7	0,21,195:7
 17	335	.	A	G,<*>	0	.	DP=32;I16=13,18,1,0,1084,40336,4,16,1589,87297,60,3600,555,11943,0,0;QS=2.98919,0.0108108,0;SGB=-0.556633;RPBZ=-1.67921;MQBZ=0.622171;MQSBZ=-2.25492;BQBZ=-1.68602;SCBZ=-0.258065;FS=0;MQ0F=0	PL:DP:DV	0,33,252,33,252,252:11:0	0,27,219,27,219,219:9:0	0,25,245,33,248,245:12:1
 17	336	.	A	<*>	.	.	MinDP=9;QS=3,0	PL:DP	0,33,255:11	0,27,212:9	0,36,255:12
