Un-balanced paternal/maternal haplotigs from trio binning (Revio HG002 HiFi child + NGS parental) about hifiasm HOT 2 CLOSED

I guess the main reason is that yak cannot handle bam, so it would be better to covert bam to fastq first.

from hifiasm.

Hi @chhylp123

Thank you for your help. The unbalanced haplotigs after trio-binning got fixed after switching yak input to fastq format. Yak completed nicely without complaining about the input format, I overlooked it actually did not do the job with bam files.

Now the figures make sense to me, trio-binning improved the phasing generating longer maternal haplotigs. The collapsed primary consensus contigs is almost equal size (or slightly longer) as trio-binning phased haplotigs.

Close the case. Feel free to re-open if you have any comments @chhylp123

Best regards,
Xingliang

from hifiasm.