Reg: Absence of length in certain variation events

[harish0201]

Hi!

I was annotating the SV calls from Parliament2 when I realized that the Insertion events have 0 length in the tabulated output. Is there a way that we can add the Average length from the SV VCF?

Here is a minimal example

1. VCF:

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	T8B
chr1	150880	DEL0011SUR	N	<DEL>	6	PASS	SUPP=1;SUPP_VEC=00001;AVGLEN=66;SVTYPE=DEL;SVMETHOD=SURVIVORv2;CHR2=chr1;END=150946;CIPOS=0,0;CIEND=0,0;STRANDS=+-;CALLERS=MANTA	GT:SP	0/1:MANTA
chr1	295428	TRA00406SUR	N	N[chr19:295428[>	.	PASS	SUPP=1;SUPP_VEC=00001;AVGLEN=100000;SVTYPE=BND;SVMETHOD=SURVIVORv2;CHR2=chr19;END=295428;CIPOS=0,0;CIEND=0,0;STRANDS=++;CALLERS=MANTAGT:SP	0/1:MANTA
chr1	341697	INS0013SUR	N	<INS>	.	PASS	SUPP=1;SUPP_VEC=00001;AVGLEN=59;SVTYPE=INS;SVMETHOD=SURVIVORv2;CHR2=chr1;END=341697;CIPOS=0,0;CIEND=0,0;STRANDS=+-;CALLERS=MANTA	GT:SP	1/1:MANTA
chr1	341785	TRA0014SUR	N	N[chr7:72261928[>	.	PASS	SUPP=1;SUPP_VEC=00001;AVGLEN=100000;SVTYPE=BND;SVMETHOD=SURVIVORv2;CHR2=chr7;END=72261928;CIPOS=0,0;CIEND=0,0;STRANDS=++;CALLERS=MANTAGT:SP	0/1:MANTA
chr1	380129	DEL0015SUR	N	<DEL>	6	PASS	SUPP=4;SUPP_VEC=10111;AVGLEN=6001;SVTYPE=DEL;SVMETHOD=SURVIVORv2;CHR2=chr1;END=386165;CIPOS=-11,116;CIEND=-12,0;STRANDS=+-;CALLERS=BREAKDANCER,DELLY,LUMPY,MANTA	GT:SP	1/1:BREAKDANCER,DELLY,LUMPY,MANTA

2. SANSA output:

[1]ANNOID	query.chr	query.start	query.chr2	query.end	query.id	query.qual	query.svtype	query.ct	query.svlen	query.startfeature	query.endfeature	query.containedfeature	Gene Fusion
id000000004	chr1	150880	chr1	150946	DEL0011SUR	6	DEL	3to5	66	NA	NA	NA	False
id000000005	chr1	295428	chr19	295428	TRA00406SUR	0	BND	3to3	0	NA	NA	NA	False
id000000006	chr1	341697	chr1	341697	INS0013SUR	0	INS	NtoN	0	NA	NA	NA	False
id000000007	chr1	341785	chr7	72261928	TRA0014SUR	0	BND	3to3	0	NA	NA	NA	False
id000000008	chr1	380129	chr1	386165	DEL0015SUR	6	DEL	3to5	6036	LOC100685782(0;-)	LOC100685782(0;-)	NA	False

The last column is just my label to see if genes are fusing or not, so that can be ignored.

Would it be possible to add this average length of insertion to the SANSA annotation?