AF_REF.COLOR	0,0,220
AF_VAR.COLOR	255,0,0
AUTO_UPDATE_GENOMES	true
BACKGROUND_COLOR	250,250,250
BLAT_URL	http://genome.cse.ucsc.edu/cgi-bin/hgBlat
BYPASS_FILE_AUTO_DISCOVERY	false
CBIO_AMPLIFICATION_THRESHOLD	0.9
CBIO_DELETION_THRESHOLD	0.9
CBIO_EXPRESSION_DOWN_THRESHOLD	1.0
CBIO_EXPRESSION_UP_THRESHOLD	1.0
CBIO_MUTATION_THRESHOLD	1
CHART.AUTOSCALE	false
CHART.COLOR_BORDERS	true
CHART.COLOR_TRACK_NAME	true
CHART.DRAW_AXIS	false
CHART.DRAW_BOTTOM_BORDER	false
CHART.DRAW_TOP_BORDER	false
CHART.DRAW_TRACK_NAME	false
CHART.SHOW_ALL_HEATMAP	false
CHART.SHOW_DATA_RANGE	true
CHECK_VERSION	true
CN_FREQ.AMP_THRESHOLD	0.1
CN_FREQ.DEL_THRESHOLD	-0.1
COLOR.A	0,150,0
COLOR.C	0,0,255
COLOR.G	209,113,5
COLOR.N	128,128,128
COLOR.T	255,0,0
COVER_OVERLAY_KEY	false
DB_ENABLED	false
DB_HOST	
DB_NAME	
DB_PORT	-1
DEFAULT_FONT_ATTRIBUTE	0
DEFAULT_FONT_FAMILY	Arial
DEFAULT_FONT_SIZE	10
DEFAULT_GENOME_KEY	hg19
DEFAULT_VISIBILITY_WINDOW	-1
DETAILS_BEHAVIOR	HOVER
ENABLE_ANTIALIASING	true
ENABLE_EXOME_BUTTON	false
ENABLE_GOOGLE_MENU	false
EXPAND_FEATURE_TRACKS	false
FLANKING_REGION	2000
GENE_LIST_BED_FORMAT	false
GENOME_SPACE_ATM_SERVER	https://atm.genomespace.org/atm/v1.0/
GENOME_SPACE_DM_SERVER	https://dm.genomespace.org/datamanager/v1.0/
GENOME_SPACE_ENABLE	true
GENOME_SPACE_IDENTITY_SERVER	https://identitydev.genomespace.org:8444/identityServer/basic
GWAS_ALTERNATING_COLORS	false
GWAS_DESCRIPTION_CACHE_SIZE	10000
GWAS_MAX_POINT_SIZE	7
GWAS_MIN_POINT_SIZE	3
GWAS_PRIMARY_COLOR	69,101,183
GWAS_SECONDARY_COLOR	250,169,10
GWAS_SHOW_AXIS	true
GWAS_SINGLE_COLOR	false
GWAS_TRACK_HEIGHT	200
GWAS_USE_CHR_COLORS	true
HETVAR.COLOR	0,0,255
HOMREF.COLOR	235,235,235
HOMVAR.COLOR	0,245,255
IGV.chart.track.height	40
IGV.genome.sequence.dir	http://igv.broadinstitute.org/genomes/genomes.txt
IGV.join.adjacent.segments	false
IGV.single.track.pane	false
IGV.track.height	15
IGV.track.show.attribute.views	true
IGV.track.show.missing.data	false
IONTORRENT.FLOWDIST_BINSIZE	15
IONTORRENT.FLOWDIST_CHARTTYPE	LINE
IONTORRENT.FLOWDIST_HIDE_FIRST_HP	true
IONTORRENT.RESULTS	/results/analysis/output/Home/
IONTORRENT.SERVER	ioneast.ite
MASTER_RESOURCE_FILE_KEY	http://data.broadinstitute.org/igvdata/$$_dataServerRegistry.txt
MAX_SEQUENCE_RESOLUTION	2
MUTATION_INDEL_COLOR_KEY	0,200,0
MUTATION_MISSENSE_COLOR_KEY	170,20,240
MUTATION_NONSENSE_COLOR_KEY	50,30,75
MUTATION_Non-coding_Transcript_COLOR	0,0,150
MUTATION_Other_AA_changing_COLOR	0,150,150
MUTATION_Other_likely_neutral_COLOR	225,180,225
MUTATION_SPLICE_SITE_COLOR_KEY	150,0,150
MUTATION_SYNONYMOUS_COLOR_KEY	200,170,200
MUTATION_TARGETED_REGION_COLOR_KEY	236,155,43
MUTATION_Truncating_COLOR	150,0,0
MUTATION_UNKNOWN_COLOR_KEY	0,180,225
NAME_PANEL_WIDTH	160
NOCALL.COLOR	255,255,255
NORMALIZE_COVERAGE	false
OVERLAY_ATTRIBUTE_KEY	LINKING_ID
OVERLAY_MUTATIONS_WHOLE_GENOME	true
OVERLAY_TRACKS_KEY	true
PORT_ENABLED	true
PORT_NUMBER	60151
PROBE_MAPPING_FILE	null
PROBE_MAPPING_KEY	false
PROXY.AUTHENTICATE	false
PROXY.USE	false
SAM.ALLELE_THRESHOLD	0.2f
SAM.ALLELE_USE_QUALITY	true
SAM.AUTOSORT	false
SAM.BASE_QUALITY_MAX	20
SAM.BASE_QUALITY_MIN	5
SAM.BISULFITE_CONTEXT	CG
SAM.COLOR.A	0,255,0
SAM.COLOR.C	0,0,255
SAM.COLOR.G	209,113,5
SAM.COLOR.N	182,182,182
SAM.COLOR.T	255,0,0
SAM.COLOR_BY	UNEXPECTED_PAIR
SAM.COLOR_BY_TAG
SAM.COMPUTE_ISIZES	true
SAM.COUNT_DELETED_BASES_COVERED	false
SAM.DOWNSAMPLE_READS	true
SAM.FILTER_ALIGNMENTS	false
SAM.FILTER_FAILED_READS	true
SAM.FILTER_SECONDARY_ALIGNMENTS	false
SAM.FILTER_SUPPLEMENTARY_ALIGNMENTS	false
SAM.FILTER_URL	null
SAM.FLAG_LARGE_INSERTIONS	false
SAM.FLAG_UNMAPPED_PAIR	false
SAM.FLAG_ZERO_QUALITY	true
SAM.GROUP_BY_TAG	
SAM.HIDDEN_TAGS	MD,SA
SAM.INSERT_SIZE_THRESHOLD	1000
SAM.ISIZE_MAX_PERCENTILE	99.5
SAM.JUNCTION_MIN_COVERAGE	1
SAM.JUNCTION_MIN_FLANKING_WIDTH	0
SAM.LARGE_INSERTIONS_THRESOLD	1
SAM.MAX_LEVELS	100
SAM.MAX_VISIBLE_RANGE	30
SAM.MIN_INDEL_SIZE	25
SAM.MIN_INSERT_SIZE_THRESHOLD	50
SAM.MIN_ISIZE_MIN_PERCENTILE	0.5
SAM.NOMESEQ_ENABLED	false
SAM.QUALITY_THRESHOLD	0
SAM.REDUCED_MEMORY_MODE	false
SAM.SAMPLING_WINDOW	50
SAM.SHADE_BASE_QUALITY	QUALITY
SAM.SHADE_CENTER	true
SAM.SHOW_ALIGNMENT_TRACK	true
SAM.SHOW_ALL_BASES	false
SAM.SHOW_CENTER_LINE	true
SAM.SHOW_COV_TRACK	true
SAM.SHOW_DUPLICATES	false
SAM.SHOW_GROUP_SEPARATOR	true
SAM.SHOW_JUNCTION_FLANKINGREGIONS	true
SAM.SHOW_JUNCTION_TRACK	false
SAM.SHOW_REF_SEQ	false
SAM.SHOW_SOFT_CLIPPED	false
SAM.SORT_BY_TAG	
SAM.SORT_OPTION	NUCLEOTIDE
SASHIMI.SHOW_COVERAGE	true
SAVE_GOOGLE_CREDENTIALS	true
SCALE_FONTS	false
SEARCH_ZOOM	true
SESSION.RELATIVE_PATH	false
SHOW_DEFAULT_TRACK_ATTRIBUTES	false
SHOW_EXPAND_ICON	false
SHOW_GENOME_SERVER_WARNING	true
SHOW_ORPHANED_MUTATIONS	true
SHOW_REGION_BARS	false
SHOW_SEQUENCE_TRANSLATION	false
SHOW_SIZE_WARNING	true
SKIP_VERSION	
TOOLTIP.DISMISS_DELAY	60000
TOOLTIP.INITIAL_DELAY	50
TOOLTIP.RESHOW_DELAY	50
UNLOAD_ON_GENOME_CHANGE	false
USE_PROBE_MAPPING_FILE	false
VARIANT_COLOR_BY_ALLELE_FREQ	true
showLOS	true