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'