SV end position not equal to the start + sv length

Structural Variation
1

Hi! Thank you for creating this great resource.

I am confused about the end position in the gnomad v4 SV VCF file. I understand CHROM and CHR2 are the start and end chromsomes and POS and END are the start and end on the first chromosome. I am looking at an ALU insertion on chr1 (CHROM and CHR2 = chr1). POS is 61303 and END is 61350. However, SVLEN is 279. Why is the end listed as only 47 bp from the start? If I want to convert this to a bed file, should I use start+SVLEN-1?

Thank you!

2

Hey, thank you for your interest!
The example indicate a DNA piece of 279bp inserted into chr1: 61303, with a 47bp deletion observed at the insertion point. When converting to bed format, you should use POS and END described in the vcf. The coordinates in the vcf files describes location on GRCh38, and insertion of 279bp does not change the breakpoints on reference genome, so you should not use start +SVLEN -1.

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