tsg 0.1.1

A tool to analyze and manipulate transcript segment graph (TSG)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40

##fileformat=VCFv4.3
##source=tsg
##INFO=<ID=CANONICAL,Number=0,Type=Flag,Description="Canonical splice site">
##INFO=<ID=NONCANONICAL,Number=0,Type=Flag,Description="Noncanonical splice site">
##INFO=<ID=BOUNDARY,Number=1,Type=String,Description="The coding exon boundary type of event, BOTH, LEFT, RIGHT, NEITHER.">
##INFO=<ID=DP1,Number=1,Type=Integer,Description="Total read depth at the breakpoint1">
##INFO=<ID=DP2,Number=1,Type=Integer,Description="Total read depth at the breakpoint2">
##INFO=<ID=SR,Number=1,Type=Integer,Description="The number of support reads for the breakpoints">
##INFO=<ID=OSR,Number=1,Type=Integer,Description="The number of support reads for the breakpoints before rescuer">
##INFO=<ID=PSI,Number=1,Type=Float,Description="Estimated Percent splice-in in the range (0,1], representing the percentage of NLS transcripts">
##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Type of approach used to detect SV">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="The type of event, DEL, TDUP, IDUP, INV, TRA.">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for END coordinate in case of a translocation">
##INFO=<ID=SVEND,Number=1,Type=Integer,Description="2nd position of the structural variant">
##INFO=<ID=END,Number=1,Type=Integer,Description="A placeholder for END coordinate in case of a translocation">
##INFO=<ID=STRAND1,Number=1,Type=String,Description="Strand for breakpoint1">
##INFO=<ID=STRAND2,Number=1,Type=String,Description="Strand for breakpoint2">
##INFO=<ID=MODE1,Number=1,Type=String,Description="Mode for softclipped reads at breakpoint1">
##INFO=<ID=MODE2,Number=1,Type=String,Description="Mode for softclipped reads at breakpoint2">
##INFO=<ID=GENE1,Number=1,Type=String,Description="Overlapped coding gene for breakpoint1">
##INFO=<ID=GENE2,Number=1,Type=String,Description="Overlapped coding gene for breakpoint2">
##INFO=<ID=MEGAEXON1,Number=.,Type=String,Description="ID for source mega exon">
##INFO=<ID=MEGAEXON2,Number=.,Type=String,Description="ID for target mega exon">
##INFO=<ID=HOMSEQ,Number=1,Type=String,Description="MicroHomology sequence">
##INFO=<ID=INSSEQ,Number=1,Type=String,Description="MicroInsertion sequence">
##INFO=<ID=TRANSCRIPT_ID,Number=.,Type=String,Description="Transcript ID">
##INFO=<ID=GENE_ID,Number=1,Type=String,Description="Gene ID">
##INFO=<ID=SR_ID,Number=.,Type=String,Description="Support read ID">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=TDUP,Description="Tandem duplication">
##ALT=<ID=IDUP,Description="Inverted duplication">
##ALT=<ID=INV,Description="Inversion">
##ALT=<ID=TRA,Description="Translocation">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT
chr1	1700	e1	.	<INV>	.	.	CHR2=chr1;SVEND=2000;
chr1	1700	e2	.	<DUP>	.	.	CHR2=chr1;SVEND=2000;
chr1	2200	e3	.	<TDUP>	.	.	CHR2=chr1;SVEND=2500;
chr1	1700	e4	.	<DUP>	.	.	CHR2=chr1;SVEND=2500;