Calling TE sequences from VCF files

1

I have run the software sniffles to call structural variants from Pacbio sequences. In the resultant VCF file, most of entries in the ALT field look like:

N[chromosome_3:7199420[

In the example above, this is actually for a variant in a different chromosome, CHR=chromosome_1 and POS=270281, so I guess this is a transponible element coming from chromosome 3 that is present in that location.

I am not familiarized with this format for the ALT field, and was wondering if there is a straightforward way to get the sequence for that element (or any other structural variant found in the VCF). Any ideas?


next-gen


sniffles


variant_calling

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