SVTYPE is Deprecated in Variant Call Format Specification
DarioS opened this issue · 3 comments
DarioS commented
GRIDSS uses SVTYPE=BND representation e.g. COLO829v003T.purple.sv.vcf. It is deprecated since Variant Call Format version 4.4.
d-cameron commented
It is. It was deprecated as it's redundant as the relevant information is already in the ALT field. GRIDSS will continue to write SVTYPE=BND to retain compatibility with tools that have not yet been updated to handle VCF4.4
DarioS commented
I thought GRIDSS wasn't yet 4.4-compliant. Should ##fileformat=VCFv4.2 be ##fileformat=VCFv4.4 in the header section?
d-cameron commented
GRIDSS uses HTSJDK which only writes VCFv4.2 so yes, technically that makes
it noncompliant. That said, the content of the actual records are compliant
with the 4.4 specifications.
…On Tue, Jun 11, 2024 at 4:00 PM Dario Strbenac ***@***.***> wrote:
I thought GRIDSS wasn't yet 4.4-compliant. Should ##fileformat=VCFv4.2 be
##fileformat=VCFv4.4 in the header section?
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