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Cases in which variants won’t be lifted and will remain primary-only, despite it being theoretically possible (yet complicated) to lift the variant:

 

1. Bi-allelic variants in which the sequence in the Luft reference genome represents an allele that is neither the REF allele nor the ALT one. However, if this variant is a SNP in which AF=1 or AC=AN the variant is nevertheless lifted.

 

2. Variants with more than 2 alleles (i.e. more than one ALT allele), in which the sequence in the Luft reference and Primary reference differ.

 

3. Complex re-arrangement variants (as defined in section 5.4 of the VCF specification).

 

4. Variants with a symbolic ALT allele (eg <DEL>) where the Luft reference and Primary reference differ and/or there is a strand reversal.

 

5. An indel variant that is not left-anchored and has a strand reversal (“left-anchored” means for example “A ACCT” - ‘A’ is the anchor base and it appears on the left, while “G CTTG” is not left-anchored).

 

Note: When running genozip --chain, a human-readable rejects file, eg mydata.d.vcf.genozip.rejects will describe the cause of each rejected variant.

Questions? support@genozip.com

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