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odelaneau / shapeit4

Segmented HAPlotype Estimation and Imputation Tool
MIT License
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Paternal and maternal haplotypes #21

Open weishwu opened 4 years ago

weishwu commented 4 years ago

How to combine the Shapeit4 phased variants across different chromosomes? Could I run Shapeit on all chromosomes together? I'm using a pedigree-based phased vcf as scaffold. The paternal/maternal assignment in the scaffold is consistent across the chromosomes (paternal allele always in front of maternal allele).

odelaneau commented 4 years ago
  1. You can only process one chromosome at a time.
  2. Nothing prevents you to merge using bcftools all chromosomes together on phasing done.
  3. S4 is blind to maternal/paternal haplotypes. It depends how you set up your scaffold. S4 will just maintain the order you gave it as input. Best,