How to get the FASTA phased genomes from the summarized VCF file?

Hi,

I would like to get the FASTA phased genome files. For that, from a vcf file, I read that the tool gatk FastaAlternateReferenceMaker works , but the summarized vcf file obtained with IsoPhase pipeline doesn’t match.

I mean, I get that main message error when I run gatk FastaAlternateReferenceMaker : The FORMAT field was provided but there is no genotype/sample data, for input source: my_file.vcf because the summarized vcf file looks like that :

##fileformat=VCFv4.2
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT
Super-Scaffold_100001   672149  .       C       T       .       PASS    DP=210;AF=0.51  GT:HQ
Super-Scaffold_100001   862122  .       A       T       .       PASS    DP=305;AF=0.5   GT:HQ
Super-Scaffold_100001   931168  .       C       A       .       PASS    DP=127;AF=0.5   GT:HQ
Super-Scaffold_100001   967240  .       C       T       .       PASS    DP=127;AF=0.5   GT:HQ

There is the FORMAT column but there is no associated genotype in my vcf. Any idea ?

[Magdoll]

Hi @pailloufat-stack , Cupcake v15.0.0 now should have a new ‘SAMPLE’ column when you call collect_all_vcf.py, see details at the wiki

Let me know if this works for you! -Liz

[Magdoll]

hi @pailloufat-stack great!