Does or can Vt provide a 'compose_blocksub' feature?

[rhdolin]

Greetings, we have a number of VCF files generated by non-MNV aware callers, but that do include phased genotypes and phase sets. Does (or can) Vt include a utility to compose MNVs out of SNVs that are in phase and within the same codon?

[rhdolin]

Sorry, let me include an example. Here is an example where these two VCF rows could potentially be 'composed' into an MNV in order to obtain a more accurate molecular consequence prediction:

chr11	47622718	.	A	C	136.77	PASS	AC=1;AF=0.500	GT:AD:DP:GQ:PGT:PID:PL:PS	0|1:29,6:36:99:0|1:47622718_A_C:165,0,1200:47622718
chr11	47622719	.	C	T	133.77	PASS	AC=1;AF=0.500	GT:AD:DP:GQ:PGT:PID:PL:PS	0|1:30,6:37:99:0|1:47622718_A_C:162,0,1242:47622718