Frequently asked errors - Illumina/paragraph GitHub Wiki

This is the page for errors that were reported by multiple users before.

VCF format issue

It is recommended to run a sanity check for the input VCF before trying to genotype with Paragraph.

The sanity check can be performed by printing each VCF field using any VCF APIs (i.e. pysam from python)

  • raise Exception("%d:%d REF != END - POS + 1" % (start, end))

    • This indicates the REF allele length is not equal to what is described by POS and END key in INFO field. Please fix the input VCF.

  • missing REF or ALT sequence

    • Check if any insertion sequence is missing for records in the input VCF.

    • Especially, Manta uses the key SVINSSEQ to represent the insertion sequence. Set --ins-info-key to SVINSSEQ if you use Manta output as the input VCF.

  • Different padding base for REF and ALT at ...

    • Check your VCF to see if at this record the padding base is the same between REF and ALT
⚠️ **GitHub.com Fallback** ⚠️