Merge pull request #27 from gatoravi/fix_variants_annotate

Fix variants annotate
griffithlab · Apr 18, 2016 · 99ade08 · 99ade08
2 parents d93b86f + 8fcbe6d
commit 99ade08
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Showing 11 changed files with 153 additions and 71 deletions.
diff --git a/src/variants/variants_annotator.cc b/src/variants/variants_annotator.cc
@@ -253,6 +253,7 @@ void VariantsAnnotator::get_variant_overlaps_spliceregion_ns(const vector<BED>&
     }
     for(uint32_t i = 0; i < exons.size(); i++) {
         if(all_exonic_space_) {
+            //The exon start and end are in 1-based
             if(variant.end >= exons[i].start && variant.end <= exons[i].end) {
                 variant.score =  common::num_to_str(min(variant.end - exons[i].start,
                                                         exons[i].end - variant.end));
@@ -261,9 +262,10 @@ void VariantsAnnotator::get_variant_overlaps_spliceregion_ns(const vector<BED>&
             }
         }
         if(all_intronic_space_) {
-            if(i != 0 && variant.end >= exons[i].start && variant.end <= exons[i].end) {
-                variant.score =  common::num_to_str(min(variant.end - exons[i].end,
-                                                        exons[i-1].start - variant.end));
+            //The exon start and end are in 1-based
+            if(i != exons.size() - 1 && variant.end < exons[i].start && variant.end > exons[i+1].end) {
+                variant.score =  common::num_to_str(min(variant.end - exons[i+1].end,
+                                                        exons[i].start - variant.end));
                 variant.annotation = "intronic";
                 return;
             }
@@ -273,10 +275,10 @@ void VariantsAnnotator::get_variant_overlaps_spliceregion_ns(const vector<BED>&
             if(exons[i].end + intronic_min_distance_ < variant.end) {
                 return;
             }
-            //exonic near start
-            if(variant.end >= exons[i].start &&
-            variant.end <= exons[i].end &&
-            variant.end <= exons[i].start + exonic_min_distance_) {
+            //exonic near start and not last exon
+            if(i != exons.size() - 1 && variant.end >= exons[i].start &&
+               variant.end <= exons[i].end &&
+               variant.end <= exons[i].start + exonic_min_distance_) {
                 variant.score =  common::num_to_str(min(variant.end - exons[i].start,
                                                         exons[i].end - variant.end));
                 variant.annotation = "splicing_exonic";
@@ -294,10 +296,11 @@ void VariantsAnnotator::get_variant_overlaps_spliceregion_ns(const vector<BED>&
                 set_variant_cis_effect_limits(exons, variant, i);
                 return;
             }
-            //exonic near end
-            if(variant.end <= exons[i].end &&
-            variant.end >= exons[i].start &&
-            variant.end >= exons[i].end - exonic_min_distance_) {
+            //exonic near end and not first exon
+            if(i != 0 &&
+               variant.end <= exons[i].end &&
+               variant.end >= exons[i].start &&
+               variant.end >= exons[i].end - exonic_min_distance_) {
                 variant.score =  common::num_to_str(min(variant.end - exons[i].start,
                                                         exons[i].end - variant.end));
                 variant.annotation = "splicing_exonic";
@@ -332,7 +335,8 @@ void VariantsAnnotator::get_variant_overlaps_spliceregion_ps(const vector<BED>&
     }
     for(uint32_t i = 0; i < exons.size(); i++) {
         if(all_exonic_space_) {
-            if(all_exonic_space_ && variant.end >= exons[i].start &&
+            //The exon start and end are in 1-based
+            if(variant.end >= exons[i].start &&
                variant.end <= exons[i].end) {
                 variant.score =  common::num_to_str(min(variant.end - exons[i].start,
                                                         exons[i].end - variant.end));
@@ -341,8 +345,9 @@ void VariantsAnnotator::get_variant_overlaps_spliceregion_ps(const vector<BED>&
             }
         }
         if(all_intronic_space_) {
-            if(all_intronic_space_ && i != exons.size() - 1 &&
-               variant.end >= exons[i].end && variant.end <= exons[i+1].start) {
+            //The exon start and end are in 1-based
+            if(i != exons.size() - 1 &&
+               variant.end > exons[i].end && variant.end < exons[i+1].start) {
                 variant.score =  common::num_to_str(min(variant.end - exons[i].end,
                                                         exons[i+1].start - variant.end));
                 variant.annotation = "intronic";
@@ -354,10 +359,11 @@ void VariantsAnnotator::get_variant_overlaps_spliceregion_ps(const vector<BED>&
             if(exons[i].start - intronic_min_distance_ > variant.end) {
                 return;
             }
-            //exonic near start
-            if(variant.end >= exons[i].start &&
-            variant.end <= exons[i].end &&
-            variant.end <= exons[i].start + exonic_min_distance_) {
+            //exonic near start and not first exon
+            if(i != 0 &&
+               variant.end >= exons[i].start &&
+               variant.end <= exons[i].end &&
+               variant.end <= exons[i].start + exonic_min_distance_) {
                 variant.score =  common::num_to_str(min(variant.end - exons[i].start,
                                                         exons[i].end - variant.end));
                 variant.annotation = "splicing_exonic";
@@ -376,9 +382,10 @@ void VariantsAnnotator::get_variant_overlaps_spliceregion_ps(const vector<BED>&
                 return;
             }
             //exonic near end
-            if(variant.end <= exons[i].end &&
-            variant.end >= exons[i].start &&
-            variant.end >= exons[i].end - exonic_min_distance_) {
+            if(i != exons.size() - 1 &&
+               variant.end <= exons[i].end &&
+               variant.end >= exons[i].start &&
+               variant.end >= exons[i].end - exonic_min_distance_) {
                 variant.score =  common::num_to_str(min(variant.end - exons[i].start,
                                                         exons[i].end - variant.end));
                 variant.annotation = "splicing_exonic";

diff --git a/tests/integration-test/data/cis-ase-identify/expected-cis-ase-identify-default.out b/tests/integration-test/data/cis-ase-identify/expected-cis-ase-identify-default.out
@@ -0,0 +1,62 @@
+
+Program:	regtools
+Version:	0.2.0
+Somatic variants: ../tests/integration-test/data/vcf/test3.vcf
+Polymorphisms: ../tests/integration-test/data/vcf/test4.vcf.gz
+Tumor DNA: ../tests/integration-test/data/bam/cis_ase_tumor_dna.bam
+Tumor RNA: ../tests/integration-test/data/bam/cis_ase_tumor_rna.bam
+Reference fasta file: ../tests/integration-test/data/fa/test_chr22.fa
+Annotation file: ../tests/integration-test/data/gtf/test_ensemble_chr22.3.gtf
+Minimum read-depth for variants: 10
+Warning: The index file is older than the data file: ../tests/integration-test/data/vcf/test4.vcf.gz.tbi
+
+somatic region is 22:1950-1950
+Region within run_mpileup 22:1950-1950
+
+Somatic het. Window is total, max 22 1950 0.759021 C
+22:949-2949
+
+inside process_snps 22:949-2949
+Warning: The index file is older than the data file: ../tests/integration-test/data/vcf/test4.vcf.gz.tbi
+Warning: The index file is older than the data file: ../tests/integration-test/data/vcf/test4.vcf.gz.tbi
+Warning: The index file is older than the data file: ../tests/integration-test/data/vcf/test4.vcf.gz.tbi
+
+snp region is 22:1050-1050
+running dna snp-mpileup
+Region within run_mpileup 22:1050-1050
+total, max 22 1050 0.665255 A
+dna is het, now running RNA snp-mpileup
+Region within run_mpileup 22:1050-1050
+RNA-hom
+total, max 22 1050 3.16228e-26 A
+potential ASE 22:1050-1050
+
+snp region is 22:1550-1550
+running dna snp-mpileup
+Region within run_mpileup 22:1550-1550
+total, max 22 1550 0.991995 C
+dna is het, now running RNA snp-mpileup
+Region within run_mpileup 22:1550-1550
+RNA-hom
+total, max 22 1550 3.16228e-26 C
+potential ASE 22:1550-1550
+
+snp region is 22:2050-2050
+running dna snp-mpileup
+Region within run_mpileup 22:2050-2050
+total, max 22 2050 0.984205 C
+dna is het, now running RNA snp-mpileup
+Region within run_mpileup 22:2050-2050
+RNA-hom
+total, max 22 2050 3.16228e-26 C
+potential ASE 22:2050-2050
+
+snp region is 22:2550-2550
+running dna snp-mpileup
+Region within run_mpileup 22:2550-2550
+total, max 22 2550 0.984205 C
+dna is het, now running RNA snp-mpileup
+Region within run_mpileup 22:2550-2550
+RNA-hom
+total, max 22 2550 3.16228e-26 C
+potential ASE 22:2550-2550
diff --git a/...plice-effects-identify/expected-cis-splice-effects-identify-default-annotatedvariants.out b/...plice-effects-identify/expected-cis-splice-effects-identify-default-annotatedvariants.out
@@ -23,11 +23,9 @@
 ##INFO=<ID=distances,Number=1,Type=String,Description="Vector of Min(Distance from start/end of exon in the transcript.)">
 ##INFO=<ID=annotations,Number=1,Type=String,Description="Does the variant fall in exonic/intronic splicing related space in the transcript.">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
-22	12791	.	C	T	59.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=0;annotations=splicing_exonic	GT:GQ	0/1:245	0/1:245
 22	38192	.	G	T	19.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=0;annotations=splicing_exonic	GT:GQ	0/1:215	0/1:225
 22	94627	.	G	C	29.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=1;annotations=splicing_intronic	GT:GQ	0/1:215	0/1:225
 22	97780	.	G	T	29.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=2;annotations=splicing_exonic	GT:GQ	0/1:215	0/1:225
-22	101080	.	G	T	29.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=2;annotations=splicing_exonic	GT:GQ	0/1:215	0/1:225
 22	167675	.	G	T	29.2	PASS	AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244,ENST00000405486,ENST00000407260,ENST00000455915;distances=2,2,2,2;annotations=splicing_exonic,splicing_exonic,splicing_exonic,splicing_exonic	GT:GQ	0/1:215	0/1:225
 22	167677	.	G	T	29.2	PASS	AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244,ENST00000405486,ENST00000407260,ENST00000455915;distances=0,0,0,0;annotations=splicing_exonic,splicing_exonic,splicing_exonic,splicing_exonic	GT:GQ	0/1:215	0/1:225
 22	167679	.	G	T	29.2	PASS	AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244,ENST00000405486,ENST00000407260,ENST00000455915;distances=2,2,2,2;annotations=splicing_intronic,splicing_intronic,splicing_intronic,splicing_intronic	GT:GQ	0/1:215	0/1:225

diff --git a/tests/integration-test/data/variants-annotate/expected-annotate-E-i6.out b/tests/integration-test/data/variants-annotate/expected-annotate-E-i6.out
@@ -33,6 +33,8 @@
 22	92500	.	G	C	29.2	PASS	AN=4;AC=2;genes=NA;transcripts=NA;distances=NA;annotations=NA	GT:GQ	0/1:215	0/1:225
 22	94627	.	G	C	29.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=1;annotations=splicing_intronic	GT:GQ	0/1:215	0/1:225
 22	94700	.	G	C	29.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=72;annotations=exonic	GT:GQ	0/1:215	0/1:225
+22	97533	.	G	T	29.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=0;annotations=exonic	GT:GQ	0/1:215	0/1:225
+22	97778	.	G	T	29.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=0;annotations=exonic	GT:GQ	0/1:215	0/1:225
 22	97780	.	G	T	29.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=2;annotations=exonic	GT:GQ	0/1:215	0/1:225
 22	100000	.	G	T	29.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=1082;annotations=exonic	GT:GQ	0/1:215	0/1:225
 22	101076	.	G	T	29.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=6;annotations=exonic	GT:GQ	0/1:215	0/1:225

diff --git a/tests/integration-test/data/variants-annotate/expected-annotate-E.out b/tests/integration-test/data/variants-annotate/expected-annotate-E.out
@@ -33,6 +33,8 @@
 22	92500	.	G	C	29.2	PASS	AN=4;AC=2;genes=NA;transcripts=NA;distances=NA;annotations=NA	GT:GQ	0/1:215	0/1:225
 22	94627	.	G	C	29.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=1;annotations=splicing_intronic	GT:GQ	0/1:215	0/1:225
 22	94700	.	G	C	29.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=72;annotations=exonic	GT:GQ	0/1:215	0/1:225
+22	97533	.	G	T	29.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=0;annotations=exonic	GT:GQ	0/1:215	0/1:225
+22	97778	.	G	T	29.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=0;annotations=exonic	GT:GQ	0/1:215	0/1:225
 22	97780	.	G	T	29.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=2;annotations=exonic	GT:GQ	0/1:215	0/1:225
 22	100000	.	G	T	29.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=1082;annotations=exonic	GT:GQ	0/1:215	0/1:225
 22	101076	.	G	T	29.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=6;annotations=exonic	GT:GQ	0/1:215	0/1:225

diff --git a/tests/integration-test/data/variants-annotate/expected-annotate-I.out b/tests/integration-test/data/variants-annotate/expected-annotate-I.out
@@ -24,32 +24,34 @@
 ##INFO=<ID=annotations,Number=1,Type=String,Description="Does the variant fall in exonic/intronic splicing related space in the transcript.">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
 22	12785	.	C	T	59.2	PASS	AN=4;AC=2;genes=NA;transcripts=NA;distances=NA;annotations=NA	GT:GQ	0/1:245	0/1:245
-22	12791	.	C	T	59.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=0;annotations=splicing_exonic	GT:GQ	0/1:245	0/1:245
+22	12791	.	C	T	59.2	PASS	AN=4;AC=2;genes=NA;transcripts=NA;distances=NA;annotations=NA	GT:GQ	0/1:245	0/1:245
 22	12797	.	C	T	59.2	PASS	AN=4;AC=2;genes=NA;transcripts=NA;distances=NA;annotations=NA	GT:GQ	0/1:245	0/1:245
 22	14010	.	C	T	59.2	PASS	AN=4;AC=2;genes=NA;transcripts=NA;distances=NA;annotations=NA	GT:GQ	0/1:245	0/1:245
 22	17750	.	G	T	19.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=3647;annotations=intronic	GT:GQ	0/1:215	0/1:225
-22	38192	.	G	T	19.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=0;annotations=intronic	GT:GQ	0/1:215	0/1:225
+22	38192	.	G	T	19.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=0;annotations=splicing_exonic	GT:GQ	0/1:215	0/1:225
 22	47048	.	G	T	29.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=3;annotations=intronic	GT:GQ	0/1:215	0/1:225
-22	92500	.	G	C	29.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=924;annotations=intronic	GT:GQ	0/1:215	0/1:225
-22	94627	.	G	C	29.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=1;annotations=intronic	GT:GQ	0/1:215	0/1:225
-22	94700	.	G	C	29.2	PASS	AN=4;AC=2;genes=NA;transcripts=NA;distances=NA;annotations=NA	GT:GQ	0/1:215	0/1:225
-22	97780	.	G	T	29.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=2;annotations=splicing_exonic	GT:GQ	0/1:215	0/1:225
-22	100000	.	G	T	29.2	PASS	AN=4;AC=2;genes=NA;transcripts=NA;distances=NA;annotations=NA	GT:GQ	0/1:215	0/1:225
-22	101076	.	G	T	29.2	PASS	AN=4;AC=2;genes=NA;transcripts=NA;distances=NA;annotations=NA	GT:GQ	0/1:215	0/1:225
-22	101080	.	G	T	29.2	PASS	AN=4;AC=2;genes=EP300;transcripts=ENST00000263253;distances=2;annotations=splicing_exonic	GT:GQ	0/1:215	0/1:225
-22	101088	.	G	T	29.2	PASS	AN=4;AC=2;genes=NA;transcripts=NA;distances=NA;annotations=NA	GT:GQ	0/1:215	0/1:225
-22	104067	.	G	T	29.2	PASS	AN=4;AC=2;genes=RP1-85F18.6;transcripts=ENST00000415054;distances=1;annotations=splicing_intronic	GT:GQ	0/1:215	0/1:225
+22	92500	.	G	C	29.2	PASS	AN=4;AC=2;genes=EP300,RP1-85F18.6;transcripts=ENST00000263253,ENST00000415054;distances=924,1914;annotations=intronic,intronic	GT:GQ	0/1:215	0/1:225
+22	94627	.	G	C	29.2	PASS	AN=4;AC=2;genes=EP300,RP1-85F18.6;transcripts=ENST00000263253,ENST00000415054;distances=1,4041;annotations=intronic,intronic	GT:GQ	0/1:215	0/1:225
+22	94700	.	G	C	29.2	PASS	AN=4;AC=2;genes=RP1-85F18.6;transcripts=ENST00000415054;distances=4114;annotations=intronic	GT:GQ	0/1:215	0/1:225
+22	97533	.	G	T	29.2	PASS	AN=4;AC=2;genes=EP300,RP1-85F18.6;transcripts=ENST00000263253,ENST00000415054;distances=0,6535;annotations=splicing_exonic,intronic	GT:GQ	0/1:215	0/1:225
+22	97778	.	G	T	29.2	PASS	AN=4;AC=2;genes=EP300,RP1-85F18.6;transcripts=ENST00000263253,ENST00000415054;distances=0,6290;annotations=splicing_exonic,intronic	GT:GQ	0/1:215	0/1:225
+22	97780	.	G	T	29.2	PASS	AN=4;AC=2;genes=EP300,RP1-85F18.6;transcripts=ENST00000263253,ENST00000415054;distances=2,6288;annotations=splicing_exonic,intronic	GT:GQ	0/1:215	0/1:225
+22	100000	.	G	T	29.2	PASS	AN=4;AC=2;genes=RP1-85F18.6;transcripts=ENST00000415054;distances=4068;annotations=intronic	GT:GQ	0/1:215	0/1:225
+22	101076	.	G	T	29.2	PASS	AN=4;AC=2;genes=RP1-85F18.6;transcripts=ENST00000415054;distances=2992;annotations=intronic	GT:GQ	0/1:215	0/1:225
+22	101080	.	G	T	29.2	PASS	AN=4;AC=2;genes=RP1-85F18.6;transcripts=ENST00000415054;distances=2988;annotations=intronic	GT:GQ	0/1:215	0/1:225
+22	101088	.	G	T	29.2	PASS	AN=4;AC=2;genes=RP1-85F18.6;transcripts=ENST00000415054;distances=2980;annotations=intronic	GT:GQ	0/1:215	0/1:225
+22	104067	.	G	T	29.2	PASS	AN=4;AC=2;genes=RP1-85F18.6;transcripts=ENST00000415054;distances=1;annotations=intronic	GT:GQ	0/1:215	0/1:225
 22	104068	.	G	T	29.2	PASS	AN=4;AC=2;genes=RP1-85F18.6;transcripts=ENST00000415054;distances=0;annotations=splicing_exonic	GT:GQ	0/1:215	0/1:225
 22	104069	.	G	T	29.2	PASS	AN=4;AC=2;genes=RP1-85F18.6;transcripts=ENST00000415054;distances=1;annotations=splicing_exonic	GT:GQ	0/1:215	0/1:225
-22	104148	.	G	T	29.2	PASS	AN=4;AC=2;genes=RP1-85F18.6;transcripts=ENST00000415054;distances=1;annotations=splicing_exonic	GT:GQ	0/1:215	0/1:225
-22	104149	.	G	T	29.2	PASS	AN=4;AC=2;genes=RP1-85F18.6;transcripts=ENST00000415054;distances=0;annotations=splicing_exonic	GT:GQ	0/1:215	0/1:225
+22	104148	.	G	T	29.2	PASS	AN=4;AC=2;genes=NA;transcripts=NA;distances=NA;annotations=NA	GT:GQ	0/1:215	0/1:225
+22	104149	.	G	T	29.2	PASS	AN=4;AC=2;genes=NA;transcripts=NA;distances=NA;annotations=NA	GT:GQ	0/1:215	0/1:225
 22	104150	.	G	T	29.2	PASS	AN=4;AC=2;genes=NA;transcripts=NA;distances=NA;annotations=NA	GT:GQ	0/1:215	0/1:225
-22	167640	.	G	T	29.2	PASS	AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244,ENST00000405486,ENST00000407260,ENST00000455915;distances=2695,2695,2695,2695;annotations=intronic,intronic,intronic,intronic	GT:GQ	0/1:215	0/1:225
-22	167675	.	G	T	29.2	PASS	AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244,ENST00000405486,ENST00000407260,ENST00000455915;distances=2660,2660,2660,2660;annotations=intronic,intronic,intronic,intronic	GT:GQ	0/1:215	0/1:225
-22	167677	.	G	T	29.2	PASS	AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244,ENST00000405486,ENST00000407260,ENST00000455915;distances=0,0,0,0;annotations=intronic,intronic,intronic,intronic	GT:GQ	0/1:215	0/1:225
-22	167679	.	G	T	29.2	PASS	AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244,ENST00000405486,ENST00000407260,ENST00000455915;distances=2,2,2,2;annotations=splicing_intronic,splicing_intronic,splicing_intronic,splicing_intronic	GT:GQ	0/1:215	0/1:225
-22	175311	.	G	T	29.2	PASS	AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244,ENST00000405486,ENST00000407260,ENST00000455915;distances=2,2,2,2;annotations=splicing_intronic,splicing_intronic,splicing_intronic,splicing_intronic	GT:GQ	0/1:215	0/1:225
-22	175501	.	G	T	29.2	PASS	AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244,ENST00000405486,ENST00000407260,ENST00000455915;distances=2,2,2,2;annotations=splicing_intronic,splicing_intronic,splicing_intronic,splicing_intronic	GT:GQ	0/1:215	0/1:225
-22	206985	.	G	T	29.2	PASS	AN=4;AC=2;genes=NA;transcripts=NA;distances=NA;annotations=NA	GT:GQ	0/1:215	0/1:225
+22	167640	.	G	T	29.2	PASS	AN=4;AC=2;genes=NA;transcripts=NA;distances=NA;annotations=NA	GT:GQ	0/1:215	0/1:225
+22	167675	.	G	T	29.2	PASS	AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244,ENST00000405486,ENST00000407260,ENST00000455915;distances=2,2,2,2;annotations=splicing_exonic,splicing_exonic,splicing_exonic,splicing_exonic	GT:GQ	0/1:215	0/1:225
+22	167677	.	G	T	29.2	PASS	AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244,ENST00000405486,ENST00000407260,ENST00000455915;distances=0,0,0,0;annotations=splicing_exonic,splicing_exonic,splicing_exonic,splicing_exonic	GT:GQ	0/1:215	0/1:225
+22	167679	.	G	T	29.2	PASS	AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244,ENST00000405486,ENST00000407260,ENST00000455915;distances=2,2,2,2;annotations=intronic,intronic,intronic,intronic	GT:GQ	0/1:215	0/1:225
+22	175311	.	G	T	29.2	PASS	AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244,ENST00000405486,ENST00000407260,ENST00000455915;distances=2,2,2,2;annotations=intronic,intronic,intronic,intronic	GT:GQ	0/1:215	0/1:225
+22	175501	.	G	T	29.2	PASS	AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244,ENST00000405486,ENST00000407260,ENST00000455915;distances=2,2,2,2;annotations=intronic,intronic,intronic,intronic	GT:GQ	0/1:215	0/1:225
+22	206985	.	G	T	29.2	PASS	AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244;distances=6;annotations=intronic	GT:GQ	0/1:215	0/1:225
 22	206991	.	G	T	29.2	PASS	AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244;distances=0;annotations=splicing_exonic	GT:GQ	0/1:215	0/1:225
 22	206993	.	G	T	29.2	PASS	AN=4;AC=2;genes=RANGAP1;transcripts=ENST00000356244;distances=2;annotations=splicing_exonic	GT:GQ	0/1:215	0/1:225