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poruloh / Eagle

Haplotype phasing software
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Phasing SVs #30

Closed jjfarrell closed 3 years ago

jjfarrell commented 3 years ago

Does eagle phasing accept VCFs with structural variants? SVs are often represented with an ALT allele of <DEL> <INS> <DUP>.The ref is sometimes set to "N" depending on the SV caller.

Or would the REF and ALT need to be filled in with the sequence? Although most are 50-500 regions, the ALT and REF alleles will include variants with 1000s of bp.

poruloh commented 3 years ago

Yes, Eagle ignores the contents of the REF and ALT fields, so it will accept a VCF file containing SVs. (If an SV spans other variants in the VCF, then the phased output could include some impossible haplotype configurations, as is also the case with multi-allelic variants.)