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##varlociraptor_preprocess_args={"Preprocess":{"kind":{"Variants":{"reference":"resources/genome.fasta","candidates":"results/candidate-calls/C-2019-03679-3A.freebayes.bcf","bam":"results/recal/C-2019-03679-3A.sorted.bam","alignment_properties":null,"output":"results/observations/C-2019-03679-3A/C-2019-03679-3A.freebayes.bcf","spurious_ins_rate":2.8e-6,"spurious_del_rate":5.1e-6,"spurious_insext_rate":0.0,"spurious_delext_rate":0.0,"protocol_strandedness":"Opposite","realignment_window":64,"max_depth":200,"omit_insert_size":true}}}}
##varlociraptor_observation_format_version=2
##INFO=<ID=PROB_FFPE_ARTIFACT,Number=A,Type=Float,Description="Posterior probability for event ffpe_artifact (PHRED)">
##INFO=<ID=PROB_PRESENT,Number=A,Type=Float,Description="Posterior probability for event present (PHRED)">
##INFO=<ID=PROB_ARTIFACT,Number=A,Type=Float,Description="Posterior probability for strand bias artifact (PHRED)">
##INFO=<ID=PROB_ABSENT,Number=A,Type=Float,Description="Posterior probability for not having a variant (PHRED)">
##FORMAT=<ID=DP,Number=A,Type=Integer,Description="Expected sequencing depth, while considering mapping uncertainty">
##FORMAT=<ID=OBS,Number=A,Type=String,Description="Posterior odds for alt allele of each fragment as Kass Raftery scores: N=none, B=barely, P=positive, S=strong, V=very strong (lower case if probability for correct mapping of fragment is <95%)">
##FORMAT=<ID=AF,Number=A,Type=Float,Description="Maximum a posteriori probability estimate of allele frequency">
##FORMAT=<ID=SB,Number=A,Type=String,Description="Strand bias estimate: + indicates that ALT allele is associated with forward strand, - indicates that ALT allele is associated with reverse strand, - indicates no strand bias.">
##bcftools_concatVersion=1.10+htslib-1.10.2
##bcftools_concatCommand=concat -a -Ob -o results/calls/C-2019-03679-3A.bcf results/calls/C-2019-03679-3A.freebayes.bcf results/calls/C-2019-03679-3A.delly.bcf; Date=Mon Jul 13 20:42:10 2020
##bcftools_viewVersion=1.9+htslib-1.9
##bcftools_viewCommand=view results/calls/C-2019-03679-3A.bcf; Date=Mon Jul 13 20:42:12 2020
##VEP="v100" time="2020-07-13 20:42:12" cache="resources/vep/cache/homo_sapiens/98_GRCh38" ensembl-funcgen=100.f0c3948 ensembl-variation=100.b220ff4 ensembl=100.7e964b7 ensembl-io=100.f87ae4f 1000genomes="phase3" COSMIC="89" ClinVar="201907" ESP="V2-SSA137" HGMD-PUBLIC="20184" assembly="GRCh38.p13" dbSNP="152" gencode="GENCODE 32" genebuild="2014-07" gnomAD="r2.1" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"
##INFO=<ID=ANN,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSg|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|MANE|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|GENE_PHENO|SIFT|PolyPhen|DOMAINS|miRNA|HGVS_OFFSET|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|AA_AF|EA_AF|gnomAD_AF|gnomAD_AFR_AF|gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|gnomAD_NFE_AF|gnomAD_OTH_AF|gnomAD_SAS_AF|MAX_AF|MAX_AF_POPS|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|LoFtool">
##LoFtool=LoFtool score for gene
##bcftools_viewCommand=view -Ob; Date=Mon Jul 13 20:42:13 2020
##bcftools_viewCommand=view -h /vol/tiny/siveke-mapktron-pdac/dna-seq-varlociraptor/results/calls/C-2019-03679-3A.annotated.bcf; Date=Tue Jul 28 11:01:12 2020
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	tumor
chr1	15	.	C	T	.	.	SVLEN=.;PROB_ARTIFACT=1266.25;PROB_ABSENT=2436.16;PROB_FFPE_ARTIFACT=801.151;PROB_PRESENT=0;ANN=T|missense_variant|MODERATE|KRAS|ENSG00000133703|Transcript|ENST00000256078|protein_coding|2/6||ENST00000256078.9:c.35G>A|ENSP00000256078.4:p.Gly12Asp|225|35|12|G/D|gGt/gAt|rs121913529&COSM1135366&COSM1140133&COSM1140134&COSM12657&COSM49168&COSM520&COSM521&COSM522||-1||SNV|HGNC|HGNC:6407|YES||1|P4|CCDS8703.1|ENSP00000256078|P01116|L7RSL8|UPI0000133132|1|deleterious(0)|benign(0.303)|Gene3D:3.40.50.300&PDB-ENSP_mappings:3gft.A&PDB-ENSP_mappings:3gft.B&PDB-ENSP_mappings:3gft.C&PDB-ENSP_mappings:3gft.D&PDB-ENSP_mappings:3gft.E&PDB-ENSP_mappings:3gft.F&PDB-ENSP_mappings:4dsn.A&PDB-ENSP_mappings:4dso.A&PDB-ENSP_mappings:4dst.A&PDB-ENSP_mappings:4dsu.A&PDB-ENSP_mappings:4epr.A&PDB-ENSP_mappings:4ept.A&PDB-ENSP_mappings:4epv.A&PDB-ENSP_mappings:4epw.A&PDB-ENSP_mappings:4epx.A&PDB-ENSP_mappings:4epy.A&PDB-ENSP_mappings:4l8g.A&PDB-ENSP_mappings:4ldj.A&PDB-ENSP_mappings:4lpk.A&PDB-ENSP_mappings:4lpk.B&PDB-ENSP_mappings:4lrw.A&PDB-ENSP_mappings:4lrw.B&PDB-ENSP_mappings:4luc.A&PDB-ENSP_mappings:4luc.B&PDB-ENSP_mappings:4lv6.A&PDB-ENSP_mappings:4lv6.B&PDB-ENSP_mappings:4lyf.A&PDB-ENSP_mappings:4lyf.B&PDB-ENSP_mappings:4lyf.C&PDB-ENSP_mappings:4lyh.A&PDB-ENSP_mappings:4lyh.B&PDB-ENSP_mappings:4lyh.C&PDB-ENSP_mappings:4lyj.A&PDB-ENSP_mappings:4m1o.A&PDB-ENSP_mappings:4m1o.B&PDB-ENSP_mappings:4m1o.C&PDB-ENSP_mappings:4m1s.A&PDB-ENSP_mappings:4m1s.B&PDB-ENSP_mappings:4m1s.C&PDB-ENSP_mappings:4m1t.A&PDB-ENSP_mappings:4m1t.B&PDB-ENSP_mappings:4m1t.C&PDB-ENSP_mappings:4m1w.A&PDB-ENSP_mappings:4m1w.B&PDB-ENSP_mappings:4m1w.C&PDB-ENSP_mappings:4m1y.A&PDB-ENSP_mappings:4m1y.B&PDB-ENSP_mappings:4m1y.C&PDB-ENSP_mappings:4m21.A&PDB-ENSP_mappings:4m21.B&PDB-ENSP_mappings:4m21.C&PDB-ENSP_mappings:4m22.A&PDB-ENSP_mappings:4m22.B&PDB-ENSP_mappings:4m22.C&PDB-ENSP_mappings:4nmm.A&PDB-ENSP_mappings:4obe.A&PDB-ENSP_mappings:4obe.B&PDB-ENSP_mappings:4pzy.A&PDB-ENSP_mappings:4pzy.B&PDB-ENSP_mappings:4pzz.A&PDB-ENSP_mappings:4q01.A&PDB-ENSP_mappings:4q01.B&PDB-ENSP_mappings:4q02.A&PDB-ENSP_mappings:4q03.A&PDB-ENSP_mappings:4ql3.A&PDB-ENSP_mappings:4tq9.A&PDB-ENSP_mappings:4tq9.B&PDB-ENSP_mappings:4tqa.A&PDB-ENSP_mappings:4tqa.B&PDB-ENSP_mappings:4wa7.A&PDB-ENSP_mappings:5f2e.A&PDB-ENSP_mappings:5kyk.A&PDB-ENSP_mappings:5kyk.B&PDB-ENSP_mappings:5kyk.C&PDB-ENSP_mappings:5mla.A&PDB-ENSP_mappings:5mlb.A&PDB-ENSP_mappings:5mlb.C&PDB-ENSP_mappings:5mlb.E&PDB-ENSP_mappings:5mlb.G&PDB-ENSP_mappings:5o2s.A&PDB-ENSP_mappings:5o2s.C&PDB-ENSP_mappings:5o2s.E&PDB-ENSP_mappings:5o2s.G&PDB-ENSP_mappings:5o2t.A&PDB-ENSP_mappings:5ocg.A&PDB-ENSP_mappings:5oco.A&PDB-ENSP_mappings:5oco.B&PDB-ENSP_mappings:5oco.C&PDB-ENSP_mappings:5oco.D&PDB-ENSP_mappings:5oco.E&PDB-ENSP_mappings:5oco.F&PDB-ENSP_mappings:5oct.A&PDB-ENSP_mappings:5oct.B&PDB-ENSP_mappings:5oct.C&PDB-ENSP_mappings:5oct.D&PDB-ENSP_mappings:5oct.E&PDB-ENSP_mappings:5oct.F&PDB-ENSP_mappings:5tar.A&PDB-ENSP_mappings:5tb5.A&PDB-ENSP_mappings:5tb5.C&PDB-ENSP_mappings:5ufe.A&PDB-ENSP_mappings:5ufq.A&PDB-ENSP_mappings:5ufq.B&PDB-ENSP_mappings:5uk9.A&PDB-ENSP_mappings:5uk9.B&PDB-ENSP_mappings:5uqw.A&PDB-ENSP_mappings:5uqw.B&PDB-ENSP_mappings:5us4.A&PDB-ENSP_mappings:5us4.B&PDB-ENSP_mappings:5usj.A&PDB-ENSP_mappings:5usj.B&PDB-ENSP_mappings:5usj.C&PDB-ENSP_mappings:5usj.D&PDB-ENSP_mappings:5usj.E&PDB-ENSP_mappings:5usj.F&PDB-ENSP_mappings:5v6s.A&PDB-ENSP_mappings:5v6v.A&PDB-ENSP_mappings:5v6v.B&PDB-ENSP_mappings:5v71.A&PDB-ENSP_mappings:5v71.B&PDB-ENSP_mappings:5v71.C&PDB-ENSP_mappings:5v71.D&PDB-ENSP_mappings:5v71.E&PDB-ENSP_mappings:5v71.F&PDB-ENSP_mappings:5v9l.A&PDB-ENSP_mappings:5v9l.B&PDB-ENSP_mappings:5v9l.C&PDB-ENSP_mappings:5v9o.A&PDB-ENSP_mappings:5v9u.A&PDB-ENSP_mappings:5v9u.B&PDB-ENSP_mappings:5vbm.A&PDB-ENSP_mappings:5vp7.A&PDB-ENSP_mappings:5vp7.F&PDB-ENSP_mappings:5vpi.A&PDB-ENSP_mappings:5vpi.B&PDB-ENSP_mappings:5vpy.A&PDB-ENSP_mappings:5vpy.B&PDB-ENSP_mappings:5vpz.A&PDB-ENSP_mappings:5vpz.B&PDB-ENSP_mappings:5vq0.A&PDB-ENSP_mappings:5vq0.B&PDB-ENSP_mappings:5vq1.A&PDB-ENSP_mappings:5vq1.B&PDB-ENSP_mappings:5vq2.A&PDB-ENSP_mappings:5vq2.B&PDB-ENSP_mappings:5vq6.A&PDB-ENSP_mappings:5vq6.B&PDB-ENSP_mappings:5vq8.A&PDB-ENSP_mappings:5vq8.B&PDB-ENSP_mappings:5w22.A&PDB-ENSP_mappings:5w22.B&PDB-ENSP_mappings:5wha.A&PDB-ENSP_mappings:5wha.D&PDB-ENSP_mappings:5wha.G&PDB-ENSP_mappings:5wha.J&PDB-ENSP_mappings:5whb.A&PDB-ENSP_mappings:5whb.D&PDB-ENSP_mappings:5whb.G&PDB-ENSP_mappings:5whb.J&PDB-ENSP_mappings:5whd.A&PDB-ENSP_mappings:5whd.B&PDB-ENSP_mappings:5whd.C&PDB-ENSP_mappings:5whd.D&PDB-ENSP_mappings:5whe.A&PDB-ENSP_mappings:5whe.D&PDB-ENSP_mappings:5whe.G&PDB-ENSP_mappings:5whe.J&PDB-ENSP_mappings:5wlb.A&PDB-ENSP_mappings:5wlb.D&PDB-ENSP_mappings:5wpm.A&PDB-ENSP_mappings:5xco.A&PDB-ENSP_mappings:5yxz.A&PDB-ENSP_mappings:5yy1.A&PDB-ENSP_mappings:6ark.A&PDB-ENSP_mappings:6asa.A&PDB-ENSP_mappings:6ase.A&PDB-ENSP_mappings:6b0v.A&PDB-ENSP_mappings:6b0v.B&PDB-ENSP_mappings:6b0y.A&PDB-ENSP_mappings:6b0y.B&PDB-ENSP_mappings:6bof.A&PDB-ENSP_mappings:6bof.B&PDB-ENSP_mappings:6bp1.A&PDB-ENSP_mappings:6cc9.B&PDB-ENSP_mappings:6cch.B&PDB-ENSP_mappings:6ccx.B&PDB-ENSP_mappings:6epl.R&PDB-ENSP_mappings:6epm.R&PDB-ENSP_mappings:6epn.R&PDB-ENSP_mappings:6epo.R&PDB-ENSP_mappings:6epp.R&PDB-ENSP_mappings:6f76.A&PDB-ENSP_mappings:6f76.B&PDB-ENSP_mappings:6f76.C&PDB-ENSP_mappings:6f76.D&PDB-ENSP_mappings:6f76.E&PDB-ENSP_mappings:6f76.F&PDB-ENSP_mappings:6fa1.A&PDB-ENSP_mappings:6fa1.B&PDB-ENSP_mappings:6fa1.C&PDB-ENSP_mappings:6fa1.D&PDB-ENSP_mappings:6fa1.E&PDB-ENSP_mappings:6fa1.F&PDB-ENSP_mappings:6fa2.A&PDB-ENSP_mappings:6fa2.B&PDB-ENSP_mappings:6fa2.C&PDB-ENSP_mappings:6fa2.D&PDB-ENSP_mappings:6fa2.E&PDB-ENSP_mappings:6fa2.F&PDB-ENSP_mappings:6fa3.A&PDB-ENSP_mappings:6fa3.B&PDB-ENSP_mappings:6fa3.C&PDB-ENSP_mappings:6fa3.D&PDB-ENSP_mappings:6fa3.E&PDB-ENSP_mappings:6fa3.F&PDB-ENSP_mappings:6fa4.A&PDB-ENSP_mappings:6fa4.B&PDB-ENSP_mappings:6fa4.C&PDB-ENSP_mappings:6fa4.D&PDB-ENSP_mappings:6fa4.E&PDB-ENSP_mappings:6fa4.F&PDB-ENSP_mappings:6god.A&PDB-ENSP_mappings:6goe.A&PDB-ENSP_mappings:6gof.A&PDB-ENSP_mappings:6gog.A&PDB-ENSP_mappings:6gog.B&PDB-ENSP_mappings:6gog.C&PDB-ENSP_mappings:6gog.D&PDB-ENSP_mappings:6gog.E&PDB-ENSP_mappings:6gog.F&PDB-ENSP_mappings:6gom.A&PDB-ENSP_mappings:6gom.B&PDB-ENSP_mappings:6gom.C&PDB-ENSP_mappings:6gom.D&PDB-ENSP_mappings:6gom.E&PDB-ENSP_mappings:6gom.F&PDB-ENSP_mappings:6gqt.A&PDB-ENSP_mappings:6gqt.B&PDB-ENSP_mappings:6gqt.C&PDB-ENSP_mappings:6gqt.D&PDB-ENSP_mappings:6gqt.E&PDB-ENSP_mappings:6gqt.F&PDB-ENSP_mappings:6gqw.A&PDB-ENSP_mappings:6gqw.B&PDB-ENSP_mappings:6gqw.C&PDB-ENSP_mappings:6gqw.D&PDB-ENSP_mappings:6gqw.E&PDB-ENSP_mappings:6gqw.F&PDB-ENSP_mappings:6gqx.A&PDB-ENSP_mappings:6gqx.B&PDB-ENSP_mappings:6gqx.C&PDB-ENSP_mappings:6gqx.D&PDB-ENSP_mappings:6gqx.E&PDB-ENSP_mappings:6gqx.F&PDB-ENSP_mappings:6gqy.A&PDB-ENSP_mappings:6gqy.B&PDB-ENSP_mappings:6gqy.C&PDB-ENSP_mappings:6gqy.D&PDB-ENSP_mappings:6gqy.E&PDB-ENSP_mappings:6gqy.F&PDB-ENSP_mappings:6h46.A&PDB-ENSP_mappings:6h47.A&PDB-ENSP_mappings:6n2j.A&PDB-ENSP_mappings:6n2k.A&Pfam:PF00071&Prints:PR00449&PROSITE_profiles:PS51421&PANTHER:PTHR24070&PANTHER:PTHR24070:SF388&SMART:SM00173&SMART:SM00174&SMART:SM00175&SMART:SM00176&Superfamily:SSF52540&TIGRFAM:TIGR00231&CDD:cd04138&Low_complexity_(Seg):seg|||||||||||4.011e-06|0|0|0|0|0|8.883e-06|0|0|8.883e-06|gnomAD_NFE|pathogenic&likely_pathogenic|0&1&1&1&1&1&1&1&1|1&1&1&1&1&1&1&1&1|25157968&19029981&22499344&17332249&21079152&2278970&3122217&12460918&16434492&19075190&22407852&17384584&18794081&19047918&19255327&19773371&23406027&22683711&19018267&21975775&17704260&15696205&16361624&16618717&18316791&19114683&19679400&20921462&20921465&21228335&19794967&21398618&23182985&7773929&8439212&15842656&17910045&19358724&19881948&20609353&20805368&20949522&21169357&22025163&22235099&22282465&22897852&23014527&25044103&26372703&27872090&29525983&30463544|||||0.19,T|missense_variant|MODERATE|KRAS|ENSG00000133703|Transcript|ENST00000311936|protein_coding|2/5||ENST00000311936.8:c.35G>A|ENSP00000308495.3:p.Gly12Asp|225|35|12|G/D|gGt/gAt|rs121913529&COSM1135366&COSM1140133&COSM1140134&COSM12657&COSM49168&COSM520&COSM521&COSM522||-1||SNV|HGNC|HGNC:6407|||1|A1|CCDS8702.1|ENSP00000308495|P01116|A0A024RAV5|UPI0000001252|1|deleterious(0)|benign(0.21)|Low_complexity_(Seg):seg&PROSITE_profiles:PS51421&CDD:cd04138&PANTHER:PTHR24070&PANTHER:PTHR24070:SF186&Pfam:PF00071&TIGRFAM:TIGR00231&Gene3D:3.40.50.300&SMART:SM00173&SMART:SM00174&SMART:SM00175&Superfamily:SSF52540&Prints:PR00449|||||||||||4.011e-06|0|0|0|0|0|8.883e-06|0|0|8.883e-06|gnomAD_NFE|pathogenic&likely_pathogenic|0&1&1&1&1&1&1&1&1|1&1&1&1&1&1&1&1&1|25157968&19029981&22499344&17332249&21079152&2278970&3122217&12460918&16434492&19075190&22407852&17384584&18794081&19047918&19255327&19773371&23406027&22683711&19018267&21975775&17704260&15696205&16361624&16618717&18316791&19114683&19679400&20921462&20921465&21228335&19794967&21398618&23182985&7773929&8439212&15842656&17910045&19358724&19881948&20609353&20805368&20949522&21169357&22025163&22235099&22282465&22897852&23014527&25044103&26372703&27872090&29525983&30463544|||||0.19,T|missense_variant|MODERATE|KRAS|ENSG00000133703|Transcript|ENST00000556131|protein_coding|2/3||ENST00000556131.1:c.35G>A|ENSP00000451856.1:p.Gly12Asp|212|35|12|G/D|gGt/gAt|rs121913529&COSM1135366&COSM1140133&COSM1140134&COSM12657&COSM49168&COSM520&COSM521&COSM522||-1||SNV|HGNC|HGNC:6407|||1|||ENSP00000451856||G3V4K2|UPI00001FB7B5|1|deleterious(0)|benign(0.039)|Low_complexity_(Seg):seg&PROSITE_profiles:PS51421&PANTHER:PTHR24070&PANTHER:PTHR24070:SF397&Pfam:PF00071&Gene3D:3.40.50.300&Superfamily:SSF52540&Prints:PR00449|||||||||||4.011e-06|0|0|0|0|0|8.883e-06|0|0|8.883e-06|gnomAD_NFE|pathogenic&likely_pathogenic|0&1&1&1&1&1&1&1&1|1&1&1&1&1&1&1&1&1|25157968&19029981&22499344&17332249&21079152&2278970&3122217&12460918&16434492&19075190&22407852&17384584&18794081&19047918&19255327&19773371&23406027&22683711&19018267&21975775&17704260&15696205&16361624&16618717&18316791&19114683&19679400&20921462&20921465&21228335&19794967&21398618&23182985&7773929&8439212&15842656&17910045&19358724&19881948&20609353&20805368&20949522&21169357&22025163&22235099&22282465&22897852&23014527&25044103&26372703&27872090&29525983&30463544|||||0.19,T|missense_variant|MODERATE|KRAS|ENSG00000133703|Transcript|ENST00000557334|protein_coding|2/3||ENST00000557334.5:c.35G>A|ENSP00000452512.1:p.Gly12Asp|232|35|12|G/D|gGt/gAt|rs121913529&COSM1135366&COSM1140133&COSM1140134&COSM12657&COSM49168&COSM520&COSM521&COSM522||-1||SNV|HGNC|HGNC:6407|||5|||ENSP00000452512||G3V5T7|UPI00021CF477|1|deleterious_low_confidence(0)|probably_damaging(0.969)|Gene3D:3.40.50.300&Pfam:PF00071&Prints:PR00449&PROSITE_profiles:PS51421&PANTHER:PTHR24070&PANTHER:PTHR24070:SF186&SMART:SM00173&Superfamily:SSF52540&Low_complexity_(Seg):seg|||||||||||4.011e-06|0|0|0|0|0|8.883e-06|0|0|8.883e-06|gnomAD_NFE|pathogenic&likely_pathogenic|0&1&1&1&1&1&1&1&1|1&1&1&1&1&1&1&1&1|25157968&19029981&22499344&17332249&21079152&2278970&3122217&12460918&16434492&19075190&22407852&17384584&18794081&19047918&19255327&19773371&23406027&22683711&19018267&21975775&17704260&15696205&16361624&16618717&18316791&19114683&19679400&20921462&20921465&21228335&19794967&21398618&23182985&7773929&8439212&15842656&17910045&19358724&19881948&20609353&20805368&20949522&21169357&22025163&22235099&22282465&22897852&23014527&25044103&26372703&27872090&29525983&30463544|||||0.19	DP:AF:OBS:SB	118:0.677288:38V+37V-19N-19N+3S-2S+:.