Common usage question

This is a page for frequently asked usage questions.

Can other types of SVs being genotyped with Paragraph?

• Duplications: Yes. Use as a symbolic allele. Note that Paragraph is not a CNV genotyper so the genotyping performance of duplications is, in general, lower than simple insertions and deletions
• Inversions: Yes. Use as symbolic allele.
• Translocations: Those are usually labeled as in VCFs. Previously we had support for this, but now we decided to remove this support. The reason behind this is that many BNDs can be represented more precisely as insertion/inversions. It can be dangerous to genotype a single breakpoint, without knowing what exactly it is.

Can Paragraph genotype SNPs and Indels?

Yes. We have tested it before. It works well for most of them. But some internal SV optimizations may not work for SNP and Indels.

Does Paragraph work if the SV is not accurate (i.e. breakpoint is off in the input VCF)?

Yes, somehow. But the bigger the deviation, the lower the genotyping performance. See Paragraph paper Figure 3 (https://link.springer.com/article/10.1186/s13059-019-1909-7) for a quantitative measurement.