Reconstruct SNP haplotypes from Illumina short reads

Reconstruct SNP haplotypes from Illumina short reads

1

I have whole genome sequencing data (Illumina paired-end 150bp) for a diverse set of highly polyploid accessions with various levels of ploidy (2n=6-16x). I would like to know if there is a method to get sequencing depths for combination of alleles that are shared on the same read.

For example, for three SNPs with two alleles A and G within 100bp, a given individual could have have the following SNP genotyping :

  • SNP1: depth_A=40, depth_G=60
  • SNP2: depth_A=10, depth_G=90
  • SNP3: depth_A=50, depth_G=50

I would like to obtain the following haplotype genotyping:

  • Haplotype: depth_AAA=5, depth_AAG=2,…,depth_GGG=40

I hope this was clear, thanks for your help.


SNP


haplotype

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