Sai Chen

When the full insertion sequence cannot be assembled, Manta will report the sequence near breakpoints instead. Paragraph only uses sequences around breakpoints for genotyping, so @brentp solution should work.

Yes. The graph model should work for any length of variants. We tested it out before and it works fine for most indels. But some optimizations might not work for...

This is a bam header error. Did you use the same reference fasta for generating your bam, and for running idxdepth?

Thanks for pointing this out! You're right this is because '-' is a separator. See the function at StringUtil.hh line 156. To make your pipeline more robust, I would recommend...

Could you please check if the padding is the same for REF and ALT at your VCF position 22:18588640?