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HBA1_HBA2.md

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HBA1/HBA2

For this region, Paraphase calls the total copy number of HBA1 and HBA2. Variants are called in the VCF, against HBA2 reference sequence.

Fields in the json file

  • genotype: reports the genotype of this family. Possible alleles include aa, aaa (duplication), -a (deletion) or -- (double deletion).
  • alleles_final: when possible, different copies of HBA are phased into alleles with read based phasing.

Visualizing haplotypes

To visualize phased haplotypes, load the output bam file in IGV, group reads by the HP tag and color alignments by YC tag. Green and purple represent two alleles, i.e. all haplotypes in green are on one one allele and all haplotypes in purple are on the other allele.

Reads in gray are either unassigned or consistent with more than one possible haplotype. When two haplotypes are identical over a region, there can be more than one haplotype consistent with a read, and the read is randomly assigned to a haplotype and colored in gray.

HBA example

  • The top panel shows a sample with two copies of HBA1 and two copies of HBA2, one on each allele.
  • The bottom panel shows a sample with a -a allele, where there is a deletion, leaving only one copy of HBA (hba_del_hap1).