Reference allele missing

[Akazhiel]

Hello!

I've noticed on running svim alignment that despite providing the reference that the reads were aligned to, all the reference alleles in the output VCF file are N. Is there any option to change this? Because as it stands it'd be beneficial to know which sequence has been deleted or duplicated.

Cheers!

[jakob-he]

Hi @Akazhiel

with the current version of SVIM the reference sequence of deletions is returned by default.
This was previously controlled by the --sequence_alleles parameter. However, now this is replaced by --symbolic_alleles which needs to be set in order not to return the nucleotide sequences.

As for duplications you currently need to use the two parameters --tandem_duplications_as_insertions and --interspersed_duplications_as_insertions. Then all duplications are returned as insertions and the records include the inserted nucleotide sequence.

We will certainly try to include an individual option for duplication records with the reference nucleotide sequence in future updates!

Best,
Jakob

[zhqduan]

hi @Akazhiel, --symbolic_alleles is not work in the SVIM 2.0.0, but I can run it with the parameter --sequence_alleles.