Is there any way to output REF and ALT sequence?

[LYC-vio]

Hi, after running MAMnet, I got a vcf with the following content:

...
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	.
chr1	32028	.	.	.	6	PASS	SVLEN=64;SVTYPE=INS;END=32029;RE=6	GT	1/1
chr1	90367	.	.	.	2	PASS	SVLEN=59;SVTYPE=INS;END=90368;RE=2	GT	1/1
chr1	384542	.	.	.	2	PASS	SVLEN=307;SVTYPE=INS;END=384543;RE=2	GT	1/1
chr1	385987	.	.	.	2	PASS	SVLEN=308;SVTYPE=INS;END=385988;RE=2	GT	1/1
chr1	546019	.	.	.	20	PASS	SVLEN=204;SVTYPE=INS;END=546020;RE=20	GT	1/1
chr1	605052	.	.	.	20	PASS	SVLEN=230;SVTYPE=INS;END=605053;RE=20	GT	1/1
chr1	649756	.	.	.	2	PASS	SVLEN=-50;SVTYPE=DEL;END=649806;RE=2	GT	1/1
...

Is there any parameters for MAMnet to output REF and ALT sequence?

[LYC-vio]

If not, I personally suggest you to use symbolic format, like:

...
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	.
chr1	32028	.	N	<INS>	6	PASS	SVLEN=64;SVTYPE=INS;END=32029;RE=6	GT	1/1
chr1	90367	.	N	<INS>	2	PASS	SVLEN=59;SVTYPE=INS;END=90368;RE=2	GT	1/1

[micahvista]

Dear LYC-vio:
Sorry for the late response, I have been working on the issue but with little progress. My plan is collect all query sequences supporting each SV call and produce a consensus sequence. Then try to remap the consensus sequence to reference genome and obtain the insert sequence. This approach will improve the breakpoint accuracy but currently my implementation is time consuming. I think I will fix this issue as soon as possible.
Thanks.
Hongyu Ding