Various updates to annotation

svtk/annotation/annotate.py

@@ -100,6 +100,7 @@ def annotate(sv, gencode, noncoding):
     '##INFO=<ID=COPY_GAIN,Number=.,Type=String,Description="Gene(s) on which the SV is predicted to have a copy-gain effect.">',
     '##INFO=<ID=INTRONIC,Number=.,Type=String,Description="Gene(s) where the SV was found to lie entirely within an intron.">',
     '##INFO=<ID=DUP_PARTIAL,Number=.,Type=String,Description="Gene(s) which are partially overlapped by an SV\'s duplication, such that an unaltered copy is preserved.">',
+    '##INFO=<ID=MSV_EXON_OVR,Number=.,Type=String,Description="Gene(s) on which the multiallelic SV would be predicted to have a LOF, DUP_LOF, COPY_GAIN, or DUP_PARTIAL annotation if the SV were biallelic.">',
     '##INFO=<ID=INV_SPAN,Number=.,Type=String,Description="Gene(s) which are entirely spanned by an SV\'s inversion.">',
     '##INFO=<ID=UTR,Number=.,Type=String,Description="Gene(s) for which the SV is predicted to disrupt a UTR.">',
     '##INFO=<ID=NEAREST_TSS,Number=.,Type=String,Description="Nearest transcription start site to intragenic variants.">',
@@ -155,9 +156,24 @@ def annotate_vcf(vcf, gencode, noncoding, annotated_vcf):
             fout.write(record)
             continue
 
-        for info, genelist in anno.items():
-            if genelist != 'NA':
-                record.info[info] = genelist
+        #Handle general catch-all intersection for MULTIALLELIC variants
+        if 'MULTIALLELIC' in record.filter:
+            multi_ovr = []
+            for info, genelist in anno.items():
+                if info in 'LOF DUP_LOF COPY_GAIN DUP_PARTIAL'.split():
+                    if genelist != 'NA':
+                        for gene in genelist.split(','):
+                            if gene not in multi_ovr:
+                                multi_ovr.append(gene)
+                else:
+                    if genelist != 'NA':
+                        record.info[info] = genelist
+            if len(multi_ovr) > 0:
+                record.info['MSV_EXON_OVR'] = ','.join(multi_ovr)
+        else:
+            for info, genelist in anno.items():
+                if genelist != 'NA':
+                    record.info[info] = genelist
 
         if 'NEAREST_TSS' in record.info:
             record.info['INTERGENIC'] = True

svtk/annotation/classify_effect.py

@@ -155,7 +155,7 @@ def classify_disrupt(disrupt_dict, svtype):
 
     if svtype == 'DEL':
         return classify_del(disrupt_dict)
-    if svtype == 'DUP':
+    if svtype in 'DUP MCNV'.split():
         return classify_dup(disrupt_dict)
     if svtype == 'INV':
         return classify_inv(disrupt_dict)

svtk/cli/annotate.py

@@ -13,9 +13,9 @@
 
 The following classes of genic effects are annotated as new VCF INFO fields if
 the SV meets the defined criteria:
-    1) LOF - Loss of function.
+    1) LOF (and DUP_LOF) - Loss of function.
         * Deletions are annotated LOF if they overlap any exon.
-        * Duplications are annotated LOF if they reside entirely within
+        * Duplications are annotated DUP_LOF if they reside entirely within
         a gene boundary and overlap any exon.
         * Inversions are annotated LOF if reside entirely within an exon, if
         one breakpoint falls within an exon, if they reside entirely within a