How to produce fasta sequence from haplotyping (illumina)

Question

[luc.cornet]

Hello,

I would like to produce a fasta file from haplotyping.

I have a reference sequence of 2kb and illumina PE reads, from a tetraploid organism. I see some SNPs in IGV and i would like to separate the variants in a fasta file, without parental information.

I produce VCF file with GATK haplotypecaller but failed to produce sequence with BCFtools and vcflib/vcf2fasta because my VCF file is not phased.

Could anyone help me for this ? Does anyone have a pipeline for that ?

Thanks, Luc

Answer 1

[WouterDeCoster]

For phasing I would suggest you take a look at WhatsHap or GATK ReadBackedPhasing.