snpEff: Unsupported structural variant types

Question

[shpak.max]

I've been using snpEff to annotate vcf from a GWAS, and in many instances, the program executes with the warning/error message:

java.lang.RuntimeException: Unsupported structural variant type '<CN0>'

It continues to run after this message and eventually returns an annotated vcf, but I'm not sure if this can potentially throw off the order of SNPs in the file, and secondly, if there's any straightforward way to modify the input files to prevent this.

Answer 1

[Pierre Lindenbaum]

I suggest, you change (sed) all those <CN0> with <CNV0 .

See https://github.com/pcingola/SnpEff/blob/91228572672f74a0fe1ad335b7ee87d4ad7e4a76/src/main/java/org/snpeff/vcf/VcfEntry.java#L1712

e.g:

sed 's/<CN\([0-9]*\)>/<CNV\1>/g'

[shpak.max]

Unfortunately, while it ran without a problem initially, when I checked the run screen today, I saw the following error message (and unlike the unedited version of the file, this one actually terminated rather than giving a warning and skipping to the next line:

java.lang.RuntimeException: Unimplemented method for variant type CNV

Is there some other character I need to replace CN0 with, e.g. DEL etc?