SVLEN missing in output / INSLEN in all output

[NicolaLady]

Hi,

I am using Delly on WGS from tumour-normal sample pairs.

I am currently exploring the unfiltered vcf output for all SV types and using bcftools to filter based on PASS only, PRECISE and SR tags.

I next wanted to look at the length distribution of SV type but the SVLEN info tag is missing in all.

I saw there is an "INSLEN" info tag there which makes sense for when its SVTYPE=INS, i.e., insertions but its there for all SVTYPES: deletion, inversion, dups and translocations.

Is there something I need to set for delly call -t to get the SVLEN?

Thanks so much,

Nicola

[tobiasrausch]

Hi Nicola,

HOMLEN and INSLEN are available for all SV types because these INFO fields encode the length of any micro-homology or micro-insertion found at the SV breakpoint (for all SV types). For insertions, INSLEN is indeed the length of the entire insertion.

SVLEN was up for discussion but in the end I decided against it because the VCF spec suggests it's the "Difference in length between REF and ALT alleles" which makes no sense for deletion-type SVs in cancer or inversions, for instance. For delly, SVs simply have 2 breakpoints declared as CHROM:POS and CHROM:INFO/END for intra-chromosomal SVs and CHROM:POS and INFO/CHR2:INFO/POS2 for inter-chromosomal SVs. For simple deletions, the length would be INFO/END - POS.

Best, Tobias