predictosaurus 0.2.4

Uncertainty aware haplotype based genomic variant effect prediction
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of structural variant (inclusive, 1-based).">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
##contig=<ID=OX512233.1,length=29890>
##INFO=<ID=FRAGMENT_ID,Number=.,Type=Integer,Description="Varlociraptor observations (binary encoded, meant for internal use only).">
##INFO=<ID=PROB_MAPPING,Number=.,Type=Integer,Description="Varlociraptor observations (binary encoded, meant for internal use only).">
##INFO=<ID=PROB_ALT,Number=.,Type=Integer,Description="Varlociraptor observations (binary encoded, meant for internal use only).">
##INFO=<ID=PROB_REF,Number=.,Type=Integer,Description="Varlociraptor observations (binary encoded, meant for internal use only).">
##INFO=<ID=PROB_MISSED_ALLELE,Number=.,Type=Integer,Description="Varlociraptor observations (binary encoded, meant for internal use only).">
##INFO=<ID=PROB_SAMPLE_ALT,Number=.,Type=Integer,Description="Varlociraptor observations (binary encoded, meant for internal use only).">
##INFO=<ID=PROB_DOUBLE_OVERLAP,Number=.,Type=Integer,Description="Varlociraptor observations (binary encoded, meant for internal use only).">
##INFO=<ID=PROB_HIT_BASE,Number=.,Type=Integer,Description="Varlociraptor observations (binary encoded, meant for internal use only).">
##INFO=<ID=STRAND,Number=.,Type=Integer,Description="Varlociraptor observations (binary encoded, meant for internal use only).">
##INFO=<ID=READ_ORIENTATION,Number=.,Type=Integer,Description="Varlociraptor observations (binary encoded, meant for internal use only).">
##INFO=<ID=READ_POSITION,Number=.,Type=Integer,Description="Varlociraptor observations (binary encoded, meant for internal use only).">
##INFO=<ID=SOFTCLIPPED,Number=.,Type=Integer,Description="Varlociraptor observations (binary encoded, meant for internal use only).">
##INFO=<ID=ALT_INDEL_OPERATIONS,Number=.,Type=Integer,Description="Varlociraptor observations (binary encoded, meant for internal use only).">
##INFO=<ID=PAIRED,Number=.,Type=Integer,Description="Varlociraptor observations (binary encoded, meant for internal use only).">
##INFO=<ID=PROB_HOMOPOLYMER_ARTIFACT_OBSERVABLE,Number=.,Type=Integer,Description="Varlociraptor observations (binary encoded, meant for internal use only).">
##INFO=<ID=PROB_HOMOPOLYMER_VARIANT_OBSERVABLE,Number=.,Type=Integer,Description="Varlociraptor observations (binary encoded, meant for internal use only).">
##INFO=<ID=HOMOPOLYMER_INDEL_LEN,Number=.,Type=Integer,Description="Varlociraptor observations (binary encoded, meant for internal use only).">
##INFO=<ID=IS_MAX_MAPQ,Number=.,Type=Integer,Description="Varlociraptor observations (binary encoded, meant for internal use only).">
##INFO=<ID=ALT_LOCUS,Number=.,Type=Integer,Description="Varlociraptor observations (binary encoded, meant for internal use only).">
##INFO=<ID=THIRD_ALLELE_EVIDENCE,Number=.,Type=Integer,Description="Varlociraptor observations (binary encoded, meant for internal use only).">
##varlociraptor_preprocess_args={"Preprocess":{"kind":{"Variants":{"reference":"results/orthanq/candidates/reference_genome/ncbi_dataset/data/genomic.fna","candidates":"results/orthanq/candidates/candidates.vcf","bam":"results/orthanq/preprocess/Sample_sorted.bam","report_fragment_ids":true,"atomic_candidate_variants":true,"omit_mapq_adjustment":true,"reference_buffer_size":10,"min_bam_refetch_distance":1,"alignment_properties":null,"output":"results/orthanq/preprocess/Sample_obs.bcf","propagate_info_fields":[],"protocol_strandedness":"Opposite","realignment_window":64,"max_depth":200,"omit_insert_size":false,"pairhmm_mode":"exact","log_mode":"default","output_raw_observations":null}}}}
##varlociraptor_observation_format_version=15
##bcftools_viewVersion=1.19+htslib-1.19.1
##bcftools_viewCommand=view tests/resources/observations.bcf; Date=Thu Mar 28 11:05:02 2024
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
OX512233.1	61	0	G	T	.	.	FRAGMENT_ID=44,0,0,0,1,0,0,0,256,0,0,0,0,257,0,0,0,256,1,0,0,0,513,0,0,0,256,2,0,0,0,769,0,0,0,256,3,0,0,0,1025,0,0,0,256,4,0,0,0,1281,0,0,0,256,5,0,0,0,1537,0,0,0,256,6,0,0,0,1793,0,0,0,256,7,0,0,0,2049,0,0,0,256,8,0,0,0,2305,0,0,0,256,9,0,0,0,2561,0,0,0,256,10,0,0,0,2817,0,0,0,256,11,0,0,0,3073,0,0,0,256,12,0,0,0,3329,0,0,0,256,13,0,0,0,3585,0,0,0,256,14,0,0,0,3841,0,0,0,256,15,0,0,0,4097,0,0,0,256,16,0,0,0,4353,0,0,0,256,17,0,0,0,4609,0,0,0,256,18,0,0,0,4865,0,0,0,256,19,0,0,0,5121,0,0,0,256,20,0,0,0,5377,0,0,0,256,21,0,0,0;PROB_MAPPING=44,0,0,0,1,0,13217,47398,1,0,13217,47398,1,0,46653,47491,1,0,46653,47491,1,0,14291,47186,1,0,14291,47186,1,0,17470,46853,1,0,17470,46853,1,0,29772,47653,1,0,29772,47653,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470,1,0,14258,46470;PROB_REF=44,0,0,0,1,0,47534,47313,1,0,47534,47313,1,0,29772,47653,1,0,29772,47653,1,0,15657,47441,1,0,15657,47441,1,0,1067,47364,1,0,1067,47364,1,0,47534,47313,1,0,47534,47313,1,0,47534,47313,1,0,47534,47313,1,0,29772,47653,1,0,29772,47653,1,0,47534,47313,1,0,47534,47313,1,0,47534,47313,1,0,47534,47313,1,0,47534,47313,1,0,47534,47313,1,0,15657,47441,1,0,15657,47441,1,0,1067,47364,1,0,1067,47364,1,0,13217,47398,1,0,13217,47398,1,0,47534,47313,1,0,47534,47313,1,0,1067,47364,1,0,1067,47364,1,0,13217,47398,1,0,13217,47398,1,0,47534,47313,1,0,47534,47313,1,0,1067,47364,1,0,1067,47364,1,0,1067,47364,1,0,1067,47364,1,0,47534,47313,1,0,47534,47313,1,0,47534,47313,1,0,47534,47313,1,0,1067,47364,1,0,1067,47364;PROB_ALT=44,0,0,0,0,0,51496,0,0,51496,1,0,30917,49415,1,0,30917,49415,1,0,58487,49433,1,0,58487,49433,0,0,51466,0,0,51466,0,0,51496,0,0,51496,0,0,51496,0,0,51496,1,0,30917,49415,1,0,30917,49415,0,0,51496,0,0,51496,0,0,51496,0,0,51496,0,0,51496,0,0,51496,1,0,58487,49433,1,0,58487,49433,0,0,51466,0,0,51466,1,0,37786,49437,1,0,37786,49437,0,0,51496,0,0,51496,0,0,51466,0,0,51466,1,0,37786,49437,1,0,37786,49437,0,0,51496,0,0,51496,0,0,51466,0,0,51466,0,0,51466,0,0,51466,0,0,51496,0,0,51496,0,0,51496,0,0,51496,0,0,51466,0,0,51466;PROB_MISSED_ALLELE=44,0,0,0,1,0,30327,48945,1,0,30327,48945,1,0,36267,48945,1,0,36267,48945,1,0,31440,48945,1,0,31440,48945,1,0,30616,48945,1,0,30616,48945,1,0,30327,48945,1,0,30327,48945,1,0,30327,48945,1,0,30327,48945,1,0,36267,48945,1,0,36267,48945,1,0,30327,48945,1,0,30327,48945,1,0,30327,48945,1,0,30327,48945,1,0,30327,48945,1,0,30327,48945,1,0,31440,48945,1,0,31440,48945,1,0,30616,48945,1,0,30616,48945,1,0,30981,48945,1,0,30981,48945,1,0,30327,48945,1,0,30327,48945,1,0,30616,48945,1,0,30616,48945,1,0,30981,48945,1,0,30981,48945,1,0,30327,48945,1,0,30327,48945,1,0,30616,48945,1,0,30616,48945,1,0,30616,48945,1,0,30616,48945,1,0,30327,48945,1,0,30327,48945,1,0,30327,48945,1,0,30327,48945,1,0,30616,48945,1,0,30616,48945;PROB_SAMPLE_ALT=44,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0;PROB_DOUBLE_OVERLAP=44,0,0,0,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512,0,0,64512;STRAND=44,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;READ_ORIENTATION=44,0,0,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0,8,0;SOFTCLIPPED=1537,0,0,0,0,0,0,11264,0,0,0,0;PAIRED=1537,0,0,0,65280,65535,65535,11279,0,0,0,0;READ_POSITION=44,0,0,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0,1,0;PROB_HIT_BASE=44,0,0,0,1,0,23950,49299,1,0,23950,49299,1,0,23950,49299,1,0,23950,49299,1,0,23950,49299,1,0,23950,49299,1,0,23950,49299,1,0,23950,49299,1,0,23950,49299,1,0,23950,49299,1,0,23950,49299,1,0,23950,49299,1,0,23950,49299,1,0,23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OX512233.1	64	1	C	T	.	.	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OX512233.1	66	2	C	A	.	.	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OX512233.1	82	3	A	G	.	.	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