convertGVFtoVCF/tests/input/zebrafish.gvf at b2e4449b41addf3a50c304468efcc72bfd9821f2 · EBIvariation/convertGVFtoVCF · GitHub

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##gff-version 3
##gvf-version 1.06
##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7955
##file-date 2015-07-15
##genome-build NCBI GRCz10
#Study_accession: nstd62
#Study_type: Control Set
#Display_name: Brown_et_al_2012
#Publication: PMID=22203992;Journal=Proceedings of the National Academy of Sciences of the United States of America;Paper_title=Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis.;Publication_year=2012
#Study: First_author=Kim Brown;Description=Comparative genomic hybridization analysis of 3 laboratory and one wild zebrafish populations for Copy Number Variants
#Assembly_name: GRCz10
#subject: subject_name=Wilds2-3
#subject: subject_name=Zon9
#subject: subject_name=JenMale7;subject_sex=Male
#subject: subject_name=JenMale6;subject_sex=Male
#sample: sample_name=JenMale6;subject_name=JenMale6
#sample: sample_name=Wilds2-3;subject_name=Wilds2-3
#sample: sample_name=Zon9;subject_name=Zon9
#sample: sample_name=JenMale7;subject_name=JenMale7
#testing_unknown_pragma
chromosome1	DGVa	copy_number_loss	77	78	.	+	.	ID=1;Name=nssv1412199;Alias=CNV28955;variant_call_so_id=SO:0001743;parent=nsv811094;Start_range=.,776614;End_range=786127,.;submitter_variant_call_id=CNV28955;sample_name=Wilds2-3;remap_score=.98857;Variant_seq=.
chromosome1	DGVa	copy_number_loss	127	132	.	+	.	ID=12;Name=nssv1406143;Alias=CNV22899;variant_call_so_id=SO:0001743;parent=nsv811095;Start_range=.,1277246;End_range=1320592,.;submitter_variant_call_id=CNV22899;sample_name=Zon9;remap_score=.87402;Variant_seq=.
chromosome1	DGVa	copy_number_gain	128	132	.	+	.	ID=13;Name=nssv1389474;Alias=CNV6230;variant_call_so_id=SO:0001742;parent=nsv811095;Start_range=.,1284210;End_range=1320592,.;submitter_variant_call_id=CNV6230;sample_name=JenMale7;remap_score=.69625;Variant_seq=.
chromosome1	DGVa	copy_number_gain	128	132	.	+	.	ID=14;Name=nssv1388955;Alias=CNV5711;variant_call_so_id=SO:0001742;parent=nsv811095;Start_range=.,1284210;End_range=1320592,.;submitter_variant_call_id=CNV5711;sample_name=JenMale6;remap_score=.85344;Variant_seq=.;allele_count=3