#General
SESSION.RELATIVE_PATH	Use relative paths in session files	boolean	TRUE
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	"Search for feature" padding region in bp, < 0 is interpreted as a percentage.	integer	2000	
DEFAULT_VISIBILITY_WINDOW	Default visibility window (kilobases), < 0 disables visibility window.	float	-1	

##Jump To Next Feature Options (f/b Keys)
NEXT_FIT_TO_WINDOW	Fit feature to window (with optional padding).	boolean	FALSE
NEXT_FLANKING_REGION	Padding region in bp, < 0 is interpreted as a percentage.	integer	0

##Appearance
BACKGROUND_COLOR	Background color	color	250,250,250
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.
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
TRACK_ATTRIBUTE_NAME_KEY	Sample attribute key for track names	string	null
EXPAND_FEATURE_TRACKS	Expand feature tracks	boolean	FALSE
NORMALIZE_COVERAGE	Normalize coverage data (.tdf files only)	boolean	FALSE
##Heatmaps
NO_DATA.COLOR	 No data	color	216,216,216
NO_CALL.COLOR	 No call	color	150,150,150

#Variants

##Variant Colors
HOMREF.COLOR	Homozygous reference	color	235,235,235
HOMVAR.COLOR	Homozygous variant	color	0,245,255
HETVAR.COLOR	Heterozygous variant	color	0,0,255
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

#Mutations
info	Settings on this tab apply to TCGA  "maf" and "mut" files.
##Color Options
COVER_OVERLAY_KEY	Color Mutations	boolean	TRUE
MUTATION_INDEL_COLOR_KEY	Indel	color	0,200,0
MUTATION_MISSENSE_COLOR_KEY	Missense	color	170,20,240
MUTATION_NONSENSE_COLOR_KE	Nonsense	color	50,30,75
MUTATION_SPLICE_SITE_COLOR_KEY	Splice Site	color	150,0,150
MUTATION_SYNONYMOUS_COLOR_KEY	Synonymous	color	200,170,200
MUTATION_TARGETED_REGION_COLOR_KEY	Targeted Region	color	236,155,43
MUTATION_Truncating_COLOR	Truncating	color	150,0,0
MUTATION_Non-coding_Transcript_COLOR	Non-coding Transcript	color	0,0,150
MUTATION_Other_AA_changing_COLOR	Other AA Changing	color	0,150,150
MUTATION_Other_likely_neutral_COLOR	Other Likely Neutral	color	225,180,225
MUTATION_UNKNOWN_COLOR_KEY	Unknown	color	0,180,225

#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
info	Settings for alignment tracks.  See the RNA or Third Gen tabs to override for specific types.

##Track Display
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.COLOR_BY	Color alignments by	select NONE|READ_STRAND|FIRST_OF_PAIR_STRAND|PAIR_ORIENTATION|UNEXPECTED_PAIR|INSERT_SIZE|SAMPLE|READ_GROUP|LIBRARY|MOVIE|ZMW|BISULFITE|NOMESEQ|TAG|MAPPED_SIZE|LINK_STRAND|YC_TAG	UNEXPECTED_PAIR
SAM.COLOR_BY_TAG	Color by TAG	string
SAM.GROUP_OPTION	Group alignments by	select NONE|STRAND|SAMPLE|READ_GROUP|LIBRARY|FIRST_OF_PAIR_STRAND|TAG|PAIR_ORIENTATION|MATE_CHROMOSOME|SV_ALIGNMENT|SUPPLEMENTARY|BASE_AT_POS|MOVIE|ZMW|HAPLOTYPE|READ_ORDER|LINKED|PHASE
SAM.GROUP_BY_TAG	Group by TAG	string
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.DISPLAY_MODE	Alignment display mode	string	EXPANDED
---
SAM.SHOW_MISMATCHES	Show mismatched bases	boolean	TRUE
SAM.SHOW_ALL_BASES	Show all bases	boolean	FALSE
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_CENTER_LINE	Show center line	boolean	FALSE
SAM.SHOW_SOFT_CLIPPED	Show soft-clipped bases	boolean	FALSE
---
SAM.SHADE_BASE_QUALITY	Shade mismatched bases by quality.	boolean	TRUE
SAM.BASE_QUALITY_MIN	Maximum transparency at base quality:	integer	5
SAM.BASE_QUALITY_MAX	No transparency above base quality:	integer	20
---
SAM.FLAG_LARGE_INDELS	Label indels >  threshold	boolean	TRUE
SAM.LARGE_INSERTIONS_THRESOLD	Label threshold (bases)	integer	1
---
SAM.HIDE_SMALL_INDEL	Hide indels <  indel size threshold	boolean	FALSE
SAM.SMALL_INDEL_BP_THRESHOLD	Indel size threshold (bases)	integer	0
---
SAM.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.HIDDEN_TAGS	Hide tags in popup text (comma delimited list)	string	SA,MD,XA,RG
---
SAM.LINK_BY_TAGS	Tags to be used for linking alignments (comma delimited list)	string	 
---
SAM.MAX_SOFT_CLIP	Soft clip reference extension (reference sequence is extended by this amount to show soft  clips)	integer	1000
---
SAM.FILTER_ALIGNMENTS	Filter alignments by read group	boolean	FALSE
SAM.FILTER_URL	URL or path to read group filter file	string	null

##Coverage Track Options
SAM.ALLELE_THRESHOLD	Coverage allele-fraction threshold	float	0.2
SAM.ALLELE_USE_QUALITY	Quality weight allele fraction	boolean	TRUE
SAM.BASEMOD_THRESHOLD	Base modification probability threshold (0-1)	float	0.2

##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

##Insert Size Options
SAM.COMPUTE_ISIZES	Compute insert size thresholds	boolean	FALSE
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	100000


#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	TRUE
SAM.CLIPPING_THRESHOLD	Flag clipping threshold (bases)	integer	20
---
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

#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.tsv
MASTER_RESOURCE_FILE_KEY	Data registry URL	string	https://data.broadinstitute.org/igvdata/$$_dataServerRegistry.txt
---
PROVISIONING.URL	OAuth provisioning URL	string	null
---

BLAT_URL	BLAT URL	String	http://genome.ucsc.edu/cgi-bin/hgBlat?userSeq=$SEQUENCE&type=DNA&db=$DB&output=json
---

## Tooltip
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


## JBrowse Circular View Integration  **EXPERIMENTAL FEATURE**
CIRC_VIEW_ENABLED	Enable CircView	boolean	FALSE
CIRC_VIEW_HOST	CircView host (usually localhost)	string	localhost
CIRC_VIEW_PORT	CircView port	integer	60152


##


#Hidden

SAM.SHOW_JUNCTION_FLANKINGREGIONS	FALSE
SAM.JUNCTION_MIN_FLANKING_WIDTH	0
SAM.JUNCTION_MIN_COVERAGE	1


SCORE_VARIANTS	FALSE

SAM.AUTOSORT	FALSE
SAM.SHADE_CENTER	TRUE
SAM.SHOW_REF_SEQ	FALSE

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.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
OVERLAY_TRACKS_KEY	TRUE
SHOW_ORPHANED_MUTATIONS	TRUE

OVERLAY_MUTATIONS_WHOLE_GENOME	TRUE


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
SEQUENCE_TRANSLATION_STRAND	POSITIVE
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	CLICK
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
GENE_LIST_BED_FORMAT	FALSE
showLOS	TRUE
DEBUG.PROXY	FALSE

MUTATION_INDEL_COLOR_KEY	Indel	color	0,200,0
MUTATION_MISSENSE_COLOR_KEY	Missense	color	170,20,240
MUTATION_NONSENSE_COLOR_KE	Nonsense	color	50,30,75
MUTATION_SPLICE_SITE_COLOR_KEY	Splice Site	color	150,0,150
MUTATION_SYNONYMOUS_COLOR_KEY	Synonymous	color	200,170,200
MUTATION_TARGETED_REGION_COLOR_KEY	Targeted Region	color	236,155,43
MUTATION_Truncating_COLOR	Truncating	color	150,0,0
MUTATION_Non-coding_Transcript_COLOR	Non-coding Transcript	color	0,0,150
MUTATION_Other_AA_changing_COLOR	Other AA Changing	color	0,150,150
MUTATION_Other_likely_neutral_COLO	Other Likely NeutralR	color	225,180,225
MUTATION_UNKNOWN_COLOR_KEY	Unknown	color	0,180,225

OVERLAY_ATTRIBUTE_KEY	Linking ID	string	LINKING_ID


