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andrewrech / antigen.garnish

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Accept MuTect2 VCFs with clonality estimation as standard input #85

Closed andrewrech closed 6 years ago

andrewrech commented 6 years ago

From PureCN

@leeprichman

andrewrech commented 6 years ago 
##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic event">
##INFO=<ID=VT,Number=1,Type=String,Description="Variant type, can be SNP, INS or DEL">
##INFO=<ID=set,Number=1,Type=String,Description="Source VCF for the merged record in CombineVariants">
##INFO=<ID=OnTarget,Number=1,Type=Integer,Description="1: On-target; 2: Flanking region; 0: Off-target.">
##INFO=<ID=Cosmic.CNT,Number=1,Type=Integer,Description="How many samples in Cosmic have this mutation">
##INFO=<ID=SM0,Number=1,Type=Float,Description="Somatic posterior probability, multiplicity 0">
##INFO=<ID=SM1,Number=1,Type=Float,Description="Somatic posterior probability, multiplicity 1">
##INFO=<ID=SM2,Number=1,Type=Float,Description="Somatic posterior probability, multiplicity 2">
##INFO=<ID=SM3,Number=1,Type=Float,Description="Somatic posterior probability, multiplicity 3">
##INFO=<ID=SM4,Number=1,Type=Float,Description="Somatic posterior probability, multiplicity 4">
##INFO=<ID=SM5,Number=1,Type=Float,Description="Somatic posterior probability, multiplicity 5">
##INFO=<ID=SM6,Number=1,Type=Float,Description="Somatic posterior probability, multiplicity 6">
##INFO=<ID=SM7,Number=1,Type=Float,Description="Somatic posterior probability, multiplicity 7">
##INFO=<ID=GM0,Number=1,Type=Float,Description="Germline posterior probability, multiplicity 0">
##INFO=<ID=GM1,Number=1,Type=Float,Description="Germline posterior probability, multiplicity 1">
##INFO=<ID=GM2,Number=1,Type=Float,Description="Germline posterior probability, multiplicity 2">
##INFO=<ID=GM3,Number=1,Type=Float,Description="Germline posterior probability, multiplicity 3">
##INFO=<ID=GM4,Number=1,Type=Float,Description="Germline posterior probability, multiplicity 4">
##INFO=<ID=GM5,Number=1,Type=Float,Description="Germline posterior probability, multiplicity 5">
##INFO=<ID=GM6,Number=1,Type=Float,Description="Germline posterior probability, multiplicity 6">
##INFO=<ID=GM7,Number=1,Type=Float,Description="Germline posterior probability, multiplicity 7">
##INFO=<ID=GCONTHIGH,Number=1,Type=Float,Description="Germline homozygous, reference allele contamination">
##INFO=<ID=GCONTLOW,Number=1,Type=Float,Description="Germline alt allele contamination">
##INFO=<ID=GHOMOZYGOUS,Number=1,Type=Float,Description="Germline homozygous">
##INFO=<ID=ML.SOMATIC,Number=0,Type=Flag,Description="Maximum likelihood state is a somatic state">
##INFO=<ID=ML.M,Number=1,Type=Float,Description="Maximum likelihood multiplicity">
##INFO=<ID=ML.C,Number=1,Type=Float,Description="Maximum likelihood integer copy number">
##INFO=<ID=ML.M.SEGMENT,Number=1,Type=Integer,Description="Maximum likelihood minor segment copy number">
##INFO=<ID=ML.AR,Number=1,Type=Float,Description="Expected allelic fraction of the maximum likelihood state">
##INFO=<ID=ML.LOH,Number=0,Type=Flag,Description="TRUE if segment is most likely in LOH">
##INFO=<ID=CS,Number=0,Type=Flag,Description="Sub-clonal copy number gain">
##INFO=<ID=CF,Number=1,Type=Float,Description="Cellular fraction">
##INFO=<ID=PS,Number=1,Type=Float,Description="Posterior probability variant is somatic mutation.">
##INFO=<ID=LR,Number=1,Type=Float,Description="Copy number log-ratio">
##INFO=<ID=GS,Number=1,Type=String,Description="Gene Symbol">
leeprichman commented 6 years ago

will close once tests for this are implemented in clonality branch

leeprichman commented 6 years ago

89