#General
SESSION.RELATIVE_PATH	Use relative paths in session files	boolean	FALSE
IGV.single.track.pane	Display all tracks in a single panel	boolean	FALSE
IGV.track.show.attribute.views	Show attribute panel	boolean	FALSE
SHOW_DEFAULT_TRACK_ATTRIBUTES	Show default track attributes	boolean	FALSE
SHOW_REGION_BARS	Show region-of-interest boundaries	boolean	FALSE
ENABLE_GOOGLE_MENU	Enable Google access	boolean	FALSE	Enable loading from Google apis.
FLANKING_REGION	Feature flanking region	integer	2000	< 0 interpreted as a percentage.
DEFAULT_VISIBILITY_WINDOW	Default visibility window (kilobases)	float	-1	< 0 disables visibility window
DEFAULT_FONT_FAMILY	Default font family	string	Arial
DEFAULT_FONT_SIZE	Default font size	float	10
SCALE_FONTS	Scale fonts	boolean	FALSE	Scale fonts for high resolution screens. Requires restart.
BACKGROUND_COLOR	Background color	color	250,250,250
ENABLE_ANTIALIASING	Enable anti-aliasing	boolean	TRUE

#Tracks
IGV.chart.track.height	Default numeric track height (pixels)	integer	40
IGV.track.height	Default feature track height (pixels)	integer	15
EXPAND_FEATURE_TRACKS	Expand feature tracks	boolean	FALSE
NORMALIZE_COVERAGE	Normalize coverage data (.tdf files only)	boolean	FALSE

#Variants

##Variant Colors
HOMREF.COLOR	Homozygous reference	color	235,235,235
HETVAR.COLOR	Homozygous variant	color	0,0,255
HOMVAR.COLOR	Heterozygous variant	color	0,245,255
NOCALL.COLOR	No call	color	255,255,255
AF_REF.COLOR	Allele freq - reference	color	0,0,220
AF_VAR.COLOR	Allel freq - variant	color	255,0,0
VARIANT_COLOR_BY_ALLELE_FREQ	Color by allele frequency (uncheck to color by allele fraction)	boolean	TRUE

#Charts
CHART.DRAW_TOP_BORDER	Draw top border	boolean	FALSE
CHART.DRAW_BOTTOM_BORDER	Draw bottom border	boolean	FALSE
CHART.COLOR_BORDERS	Color borders	boolean	TRUE
CHART.DRAW_TRACK_NAME	Draw track label	boolean	FALSE
CHART.DRAW_AXIS	Label Y axis	boolean	FALSE
CHART.AUTOSCALE	Continuous autoscale	boolean	FALSE
CHART.SHOW_DATA_RANGE	Show data range	boolean	TRUE
CN_FREQ.AMP_THRESHOLD	CN freq amplification threshold	float	0.1
CN_FREQ.DEL_THRESHOLD	CN freq deletion threshold	float	-0.1

#Alignments

##Track Display Options
SAM.SHOW_ALIGNMENT_TRACK	Show alignment track	boolean	TRUE
SAM.SHOW_COV_TRACK	Show coverage track	boolean	TRUE
SAM.SHOW_JUNCTION_TRACK	Show junction track	boolean	FALSE

##Downsampling
SAM.DOWNSAMPLE_READS	Downsample reads	boolean	TRUE
SAM.SAMPLING_WINDOW	Sampling window size (bases)	integer	50
SAM.MAX_LEVELS	Number of reads per window	integer	100

##Alignment Track Options

SAM.MAX_VISIBLE_RANGE	Visibility range threshold (kb)	float	30	Range at which alignments become visibile
SAM.QUALITY_THRESHOLD	Mapping quality threshold	int	0
SAM.ALIGNMENT_SCORE_THRESHOLD	Alignment score threshold	int	0
---
SAM.SHADE_BASE_QUALITY	Shade mismatched bases by quality	boolean	TRUE
SAM.BASE_QUALITY_MIN	Base quality minimum	integer	5
SAM.BASE_QUALITY_MAX	Base quality maximum	integer	20
---
SAM.SHOW_MISMATCHES	Show mismatched bases	boolean	TRUE
---
SAM.FLAG_LARGE_INDELS	Label indels > label threshold	boolean	TRUE
SAM.LARGE_INSERTIONS_THRESOLD	Label threshold (bases)	integer	1
---
SAM.HIDE_SMALL_INDEL	Hide indels < show indel threshold	boolean	FALSE
SAM.SMALL_INDEL_BP_THRESHOLD	Show indel threshold (bases)	integer	0
---
SAM.FLAG_CLIPPING	Flag clipping > flag clipping threshold	boolean	FALSE
SAM.CLIPPING_THRESHOLD	Flag clipping threshold (bases)	integer	0
---
SAM.QUICK_CONSENSUS_MODE	Quick consensus mode	boolean	FALSE
SAM.SHOW_INSERTION_MARKERS	Show insertion markers	boolean	FALSE
---
SAM.LINK_READS	Link alignments by tag	boolean	FALSE
SAM.LINK_TAG	Linking tag	string	READNAME
---
SAM.FILTER_DUPLICATES	Filter duplicate reads	boolean	TRUE
SAM.FILTER_FAILED_READS	Filter vendor failed reads	boolean	TRUE
SAM.FILTER_SECONDARY_ALIGNMENTS	Filter secondary alignments	boolean	FALSE
SAM.FILTER_SUPPLEMENTARY_ALIGNMENTS	Filter supplementary alignments	boolean	FALSE
SAM.FLAG_UNMAPPED_PAIR	Flag unmapped pairs	boolean	FALSE
SAM.SHOW_SOFT_CLIPPED	Show soft-clipped bases	boolean	FALSE
SAM.SHOW_CENTER_LINE	Show center line	boolean	FALSE
SAM.HIDDEN_TAGS	Hidden SAM tags	string	SA,MD,XA,RG
##Coverage Track Options
SAM.ALLELE_THRESHOLD	Coverage allele-fraction threshold	float	0.2f
SAM.ALLELE_USE_QUALITY	Quality weight allele fraction	boolean	TRUE
##Splice Junction Track
SAM.SHOW_JUNCTION_FLANKINGREGIONS	Show flanking regions	boolean	FALSE
SAM.JUNCTION_MIN_FLANKING_WIDTH	Minimum flanking width	integer	0
SAM.JUNCTION_MIN_COVERAGE	Minimum junction coverage	integer	1
##Insert Size Options
SAM.COMPUTE_ISIZES	Compute insert size thresholds	boolean	TRUE
SAM.MIN_ISIZE_MIN_PERCENTILE	Minimum (percentile)	float	0.5
SAM.ISIZE_MAX_PERCENTILE	Maximum (percentile)	float	99.5
SAM.MIN_INSERT_SIZE_THRESHOLD	Default minimum (bp)	float	50
SAM.INSERT_SIZE_THRESHOLD	Default maximum (bp)	float	1000

#RNA	RNA
info Settings below override defaults for RNA alignments.

##Track Display Options
SAM.SHOW_ALIGNMENT_TRACK	Show alignment track	boolean	TRUE
SAM.SHOW_COV_TRACK	Show coverage track	boolean	TRUE
SAM.SHOW_JUNCTION_TRACK	Show junction track	boolean	TRUE

SAM.MAX_VISIBLE_RANGE	Visibility range threshold (kb)	float	300	Range at which alignments become visibile

##Splice Junction Track
SAM.SHOW_JUNCTION_FLANKINGREGIONS	Show flanking regions	boolean	TRUE
SAM.JUNCTION_MIN_FLANKING_WIDTH	Minimum flanking width	integer	0
SAM.JUNCTION_MIN_COVERAGE	Minimum junction coverage	integer	1

#Third Gen	THIRD_GEN
info Settings below override defaults for 3rd-gen (PacBIO, Oxford Nanopore, ...) alignments.
SAM.MAX_VISIBLE_RANGE	Visibility range threshold (kb)	float	1000	Range at which alignments become visibile

##Downsampling
SAM.DOWNSAMPLE_READS	Downsample reads	boolean	FALSE

SAM.FLAG_LARGE_INDELS	Label indels > label threshold	boolean	TRUE
SAM.LARGE_INSERTIONS_THRESOLD	Label threshold (bases)	integer	1
---
SAM.HIDE_SMALL_INDEL	Hide indels < show indel threshold	boolean	TRUE
SAM.SMALL_INDEL_BP_THRESHOLD	Show indel threshold (bases)	integer	2
---
SAM.FLAG_CLIPPING	Flag clipping > flag clipping threshold	boolean	FALSE
SAM.CLIPPING_THRESHOLD	Flag clipping threshold (bases)	integer	0
---
SAM.QUICK_CONSENSUS_MODE	Quick consensus mode	boolean	TRUE
SAM.SHOW_INSERTION_MARKERS	Show insertion markers	boolean	TRUE
---
SAM.LINK_READS	Link alignments by tag	boolean	FALSE
SAM.LINK_TAG	Linking tag	string	READNAME

#Cram
CRAM.CACHE_SEQUENCES	Cache reference sequences	boolean	TRUE
CRAM.CACHE_SIZE	Cache size (MB)	integer	500

#Proxy
PROXY.DISABLE_CHECK	Disable check for system proxy	boolean	FALSE
PROXY.USE	Use proxy	boolean	FALSE
PROXY.HOST	Proxy host	string	null
PROXY.PORT	Proxy port	integer	0
PROXY.WHITELIST	Whitelist	string	null
PROXY.TYPE	Proxy type	select HTTP|SOCKS|DIRECT	HTTP
---
PROXY.AUTHENTICATE	Authentication required	boolean	FALSE
PROXY.USERNAME	Username	string	null
PROXY.PW	Password	string	null

#Advanced
---
PORT_ENABLED	Enable port	boolean	TRUE
PORT_NUMBER	Port number	integer	60151
---
IGV.genome.sequence.dir	Genome server URL	string	https://s3.amazonaws.com/igv.org.genomes/genomes.txt
MASTER_RESOURCE_FILE_KEY	Data registry url	string	https://data.broadinstitute.org/igvdata/$$_dataServerRegistry.txt
---
BLAT_URL	Blat url	String	http://genome.cse.ucsc.edu/cgi-bin/hgBlat
---
TOOLTIP.INITIAL_DELAY	Tooltip inital delay (ms)	integer	50
TOOLTIP.RESHOW_DELAY	Tooltip reshow delay (ms)	integer	50
TOOLTIP.DISMISS_DELAY	Tooltip dismiss delay (ms)	integer	60000
---

#Hidden
SCORE_VARIANTS	FALSE

SAM.COLOR_BY	UNEXPECTED_PAIR
SAM.AUTOSORT	FALSE
SAM.SHADE_CENTER	TRUE
SAM.SHOW_REF_SEQ	FALSE
SAM.SHADE_BASE_QUALITY	QUALITY
SAM.FILTER_ALIGNMENTS	FALSE
SAM.FILTER_URL	null
SAM.BISULFITE_CONTEXT	CG
SAM.FLAG_ZERO_QUALITY	TRUE
SAM.NOMESEQ_ENABLED	FALSE
SAM.COUNT_DELETED_BASES_COVERED	FALSE
SAM.SORT_OPTION	NUCLEOTIDE
SAM.GROUP_OPTION	NONE
SAM.COLOR_BY	UNEXPECTED_PAIR
SAM.SHOW_GROUP_SEPARATOR	TRUE
SAM.SHOW_ALL_BASES	FALSE
SAM.SHOW_MISMATCHES	TRUE
SAM.REDUCED_MEMORY_MODE	FALSE
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


SEARCH_ZOOM	TRUE
SAVE_GOOGLE_CREDENTIALS	TRUE
MAX_SEQUENCE_RESOLUTION	2
DEFAULT_FONT_ATTRIBUTE	0
TRACK_ATTRIBUTE_NAME_KEY
OVERLAY_TRACKS_KEY	TRUE
SHOW_ORPHANED_MUTATIONS	TRUE
COVER_OVERLAY_KEY	FALSE
OVERLAY_MUTATIONS_WHOLE_GENOME	TRUE
MUTATION_INDEL_COLOR_KEY	0,200,0
MUTATION_MISSENSE_COLOR_KEY	170,20,240
MUTATION_NONSENSE_COLOR_KEY	50,30,75
MUTATION_SPLICE_SITE_COLOR_KEY	150,0,150
MUTATION_SYNONYMOUS_COLOR_KEY	200,170,200
MUTATION_TARGETED_REGION_COLOR_KEY	236,155,43
MUTATION_UNKNOWN_COLOR_KEY	0,180,225
MUTATION_Truncating_COLOR	150,0,0
MUTATION_Non-coding_Transcript_COLOR	0,0,150
MUTATION_Other_AA_changing_COLOR	0,150,150
MUTATION_Other_likely_neutral_COLOR	225,180,225
PROBE_MAPPING_KEY	FALSE
PROBE_MAPPING_FILE	null
USE_PROBE_MAPPING_FILE	FALSE
CHART.SHOW_ALL_HEATMAP	FALSE
CHART.COLOR_TRACK_NAME	TRUE
IGV.track.show.attribute.views	TRUE

BYPASS_FILE_AUTO_DISCOVERY	FALSE
SHOW_GENOME_SERVER_WARNING	TRUE

OVERLAY_ATTRIBUTE_KEY	LINKING_ID
DEFAULT_GENOME_KEY	hg19
IGV.track.height	15
FLANKING_REGION	2000
SHOW_SEQUENCE_TRANSLATION	FALSE
AUTO_UPDATE_GENOMES	TRUE
GWAS_TRACK_HEIGHT	200
GWAS_DESCRIPTION_CACHE_SIZE	10000
GWAS_MIN_POINT_SIZE	3
GWAS_MAX_POINT_SIZE	7
GWAS_USE_CHR_COLORS	TRUE
GWAS_SINGLE_COLOR	FALSE
GWAS_ALTERNATING_COLORS	FALSE
GWAS_PRIMARY_COLOR	69,101,183
GWAS_SECONDARY_COLOR	250,169,10
GWAS_SHOW_AXIS	TRUE
ENABLE_ANTIALIASING	TRUE
NAME_PANEL_WIDTH	160
GENOME_SPACE_ENABLE	TRUE
GENOME_SPACE_DM_SERVER	https://dm.genomespace.org/datamanager/v1.0/
GENOME_SPACE_ATM_SERVER	https://atm.genomespace.org/atm/v1.0/
GENOME_SPACE_IDENTITY_SERVER	https://identitydev.genomespace.org:8444/identityServer/basic
DB_ENABLED	FALSE
DB_HOST
DB_NAME
DB_PORT	-1
CBIO_MUTATION_THRESHOLD	1
CBIO_AMPLIFICATION_THRESHOLD	0.9
CBIO_DELETION_THRESHOLD	0.9
CBIO_EXPRESSION_UP_THRESHOLD	1
CBIO_EXPRESSION_DOWN_THRESHOLD	1
DETAILS_BEHAVIOR	HOVER
SHOW_SIZE_WARNING	TRUE
SKIP_VERSION
COLOR.A	0,150,0
COLOR.C	0,0,255
COLOR.T	255,0,0
COLOR.G	209,113,5
COLOR.N	128,128,128

SASHIMI.SHOW_COVERAGE	TRUE
SAM.SHOW_DUPLICATES	FALSE
GENE_LIST_BED_FORMAT	FALSE
showLOS	TRUE
DEBUG.PROXY	FALSE

