Haplotype Phased Assembly Contigs to Chromosome Annotations

Question

[turcoa1]

Hello,

I have phased haplotype assemblies for human samples. The phased assemblies come in the form of haplotigs but I want to assign these haplotigs to chromosomes. After mapping haplotigs to chm13 with minimap2, I have a bam file with aligned haplotigs. I want to create a fastq from this bam file that contains the aligned haplotig reads as well as the chromosome it mapped to, and where it aligns in the header of the fastq so I can do chromosome level analysis on the haplotype assembly.

How can I create this fastq? The same haplotig can map to multiple chromosomes so how can I accurately obtain the best mapped assembly.