Entering edit mode
5.3 years ago
luc.cornet
•
0
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