Can split multiallelic calls

examples/multi_allele_example.vcf

@@ -0,0 +1,16 @@
+##fileformat=VCFv4.1
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##contig=<ID=1,length=249250621,assembly=b37>
+##reference=file:///humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37.fasta
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	father	mother	proband
+1	11900	.	A	T	100	PASS	MQ=1	GT:GQ	0/1:60	0/1:60	1/1:60
+1	879585	.	A	T	100	PASS	MQ=1	GT:GQ	0/1:60	0/0:60	0/1:60
+1	879586	.	A	T	100	PASS	MQ=1	GT:GQ	0/0:60	0/1:60	0/1:60
+1	947378	.	A	T	100	PASS	MQ=1	GT:GQ	0/0:60	0/0:60	0/1:60
+1	973348	.	G	A	100	PASS	MQ=1	GT:GQ	0/0:60	0/0:60	0/1:60
+3	879585	.	A	T	100	PASS	MQ=1	GT:GQ	0/1:60	0/0:60	0/1:60
+3	879586	.	A	T	100	PASS	MQ=1	GT:GQ	0/0:60	0/1:60	0/1:60
+3	947378	.	A	T	100	PASS	MQ=1	GT:GQ:AD:DP	0/0:60:5,7:12	0/0:60:4,6:14	0/1:60:7,8:16
+3	947379	.	A	T,C	100	PASS	MQ=1	GT:GQ:AD:DP	1/1:60:0,7,0:12	0/2:60:7,0,10:17	1/2:60:0,7,8:16
+3	973348	.	G	A	100	PASS	MQ=1	GT:GQ:TP	0/0:60:23	0/0:60	0/1:60
+3	973349	.	G	A,T	100	PASS	MQ=1	GT:GQ:TP	0/1:60:23	1/2:60	0/2:60

genmod/commands/annotate.py

@@ -146,6 +146,10 @@ def check_tabix_index(compressed_file, file_type='cadd', verbose=False):
                     is_flag=True,
                     help='Do not print the variants.'
 )
+@click.option('-split' ,'--split_variants', 
+                    is_flag=True,
+                    help='If the variants should be splitted.'
+)
 @click.option('-g' ,'--whole_gene', 
                     is_flag=True,
                     help="""If compounds should be checked in the whole gene regions. 
@@ -203,7 +207,7 @@ def check_tabix_index(compressed_file, file_type='cadd', verbose=False):
 )
 def annotate(family_file, variant_file, family_type, vep, silent, phased, strict, cadd_raw, whole_gene, 
                 annotation_dir, cadd_file, cadd_1000g, cadd_esp, cadd_indels, thousand_g, exac, outfile,
-                chr_prefix, processes, verbose):
+                chr_prefix, split_variants, processes, verbose):
     """Annotate variants in a VCF file.\n
         The main function with genmod is to annotate genetic inheritance patterns for variants in families. 
         Use flag --family together with a .ped file to describe which individuals in the vcf you wish to check inheritance for in the analysis.
@@ -226,17 +230,15 @@ def annotate(family_file, variant_file, family_type, vep, silent, phased, strict
     ######### Setup a variant parser #########
 
     if variant_file == '-':
-        variant_parser = vcf_parser.VCFParser(fsock = sys.stdin)
+        variant_parser = vcf_parser.VCFParser(fsock = sys.stdin, split_variants=split_variants)
     else:
-        variant_parser = vcf_parser.VCFParser(infile = variant_file)
+        variant_parser = vcf_parser.VCFParser(infile = variant_file, split_variants=split_variants)
 
     # These are the individuals in from the vcf file
     individuals = variant_parser.individuals
 
     head = variant_parser.metadata
 
-
-
     ######### Start to parse the ped file (if there is one) #########
 
     families = {}
@@ -347,7 +349,7 @@ def annotate(family_file, variant_file, family_type, vep, silent, phased, strict
 
     if verbosity:
         print('Number of CPU:s %s' % cpu_count())
-        print('Number of model checkers %s' % num_model_checkers)
+        print('Number of model checkers: %s' % num_model_checkers)
 
     # These are the workers that do the heavy part of the analysis
     model_checkers = [variant_consumer.VariantConsumer(variant_queue, 

genmod/variant_annotator.py

@@ -233,11 +233,12 @@ def check_vep_annotation(self, variant):
 
         annotation = set()
         # vep_info is a dictionary with genes as key and annotation as values
-        for gene in variant.get('vep_info',{}):
-            for consequence in variant['vep_info'][gene].get('Consequence', '').split('&'):
-                if consequence in self.INTERESTING_SO_TERMS:
-                    annotation.add(gene)
-
+        for allele in variant.get('vep_info',{}):
+            if allele != 'gene_ids':
+                for vep_annotation in variant['vep_info'][allele]:
+                    for consequence in vep_annotation.get('Consequence', '').split('&'):
+                        if consequence in self.INTERESTING_SO_TERMS:
+                            annotation.add(vep_annotation.get('SYMBOL', ''))
         return annotation
 
 

setup.py

@@ -24,7 +24,7 @@
     license = 'MIT License',
     install_requires=[
         'ped_parser >= 1.0', 
-        'vcf_parser == 0.8.3', 
+        'vcf_parser >= 1.0', 
         'pytabix', 
         'pytest', 
         'interval_tree',