marbl/merqury

improve phase block

LGG02 opened this issue · 1 comments

LGG02 commented

Hi @arangrhie
Thank you and the team for great QC tool. I have two questions:

  1. I have parental data from HiFi and MGI platform. I used HiFi parental data and MGI for assessment. HiFi based phasing results shows very high phaseblock N50 while MGI shows less
    phase_block

  2. From the phased_block.bed, we know the position where the switch are, any guidance on how to fix?

thank you for your valuable insights

arangrhie commented

Hi @LGG02,

Are you assessing the homopolymer compressed assembly for both platforms? Your HiFi uses paternal_compress.k31.hapmer. Can you re-plot them using non-compressed assembly with regular (not compressed) hapmers?