00:00:39.673	Reading cancer samples pedigree from file 'examples/samples_cancer_one.txt'.
##SnpEffVersion="4.1 (build 2015-01-07), by Pablo Cingolani"
##SnpEffCmd="SnpEff  -cancer -cancerSamples examples/samples_cancer_one.txt GRCh37.75 examples/cancer.vcf "
##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' ">
##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' ">
##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' ">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Patient_01_Germline	Patient_01_Somatic
1	69091	.	A	C,G	.	PASS	AC=1;ANN=G|start_lost|HIGH|OR4F5|ENSG00000186092|transcript|ENST00000335137|protein_coding|1/1|c.1A>G|p.Met1?|1/918|1/918|1/305||,G-C|start_lost|HIGH|OR4F5|ENSG00000186092|transcript|ENST00000335137|protein_coding|1/1|c.1A>G|p.Leu1?|1/918|1/918|1/305||WARNING_REF_DOES_NOT_MATCH_GENOME,C|initiator_codon_variant|LOW|OR4F5|ENSG00000186092|transcript|ENST00000335137|protein_coding|1/1|c.1A>C|p.Met1?|1/918|1/918|1/305||;LOF=(OR4F5|ENSG00000186092|1|1.00)	GT	1/0	2/1
