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simonrharris / SKA

Split Kmer Analysis
MIT License
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ska annotate --- generate a multi-sample VCF ? #20

Open tseemann opened 5 years ago

tseemann commented 5 years ago

Got this:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
CP006620        3509    .       T       C       .       .       NS=14;NS5=0,2,0,12,0
CP006620        4634    .       A       T       .       .       NS=14;NS5=12,0,0,2,0
CP006620        4937    .       C       T       .       .       NS=14;NS5=0,12,0,2,0

Expected:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO  SAMPLE1 SAMPLE2 SAMPLE3 ....
CP006620        3509    .       T       C       .       .       NS=14;NS5=0,2,0,12,0 GT 1 0 1 0 0 1 2
etc
simonrharris commented 5 years ago

This might take a little coding, but I'll try to add an option to output sample genotypes ASAP