Picard LiftoverVcf warning - input malformated

Question

[Yuri]

I'm working on liftover vcf from hg38 to hg19. I got this error message back:

Exception in thread "main" htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 906: unparsable vcf record with allele -, for input source: MYPATH

Has anyone encountered similar problem? Please share any thoughts, thanks!

Answer 1

[Pierre Lindenbaum]

- is not an allele supported by the picard/htsjdk api: https://github.com/samtools/htsjdk/blob/7719274fe370a51a24e6067de21bbe7e18c160a9/src/main/java/htsjdk/variant/variantcontext/Allele.java#L332

you could fix this by converting such alleles by N or <.> (symbolic allele)

[Yuri]

Thanks! I will try it :D