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* If you want to analyze dosage data from VCF file, the following option has to be specified: --dosage. A key word "DS" in FORMAT field in VCF file has to included accordingly. An example is in the following:
* If you want to analyze dosage data from VCF file, the following option has to be specified: --dosage. A key word "DS" in FORMAT field in VCF file has to included accordingly. An example is in the following:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT T2DG1000582 ID1 ID2 ID3
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT IDx ID1 ID2 ID3
22 16050408 37239779 T C . PASS AC=2;AN=496 GT:DS:GP ./.:.:0,0,0 ./.:.:0,0,0 ./.:.:0,0,0
22 16050408 37239779 T C . PASS AC=2;AN=496 GT:DS:GP ./.:.:0,0,0 ./.:.:0,0,0 ./.:.:0,0,0
22 16050933 37239784 G A . PASS AC=141;AN=904 GT:DS:GP 0/0:0.0:1,0,0 0/0:0.0:1,0,0 0/0:0.0:1,0,0
22 16050933 37239784 G A . PASS AC=141;AN=904 GT:DS:GP 0/0:0.0:1,0,0 0/0:0.0:1,0,0 0/0:0.0:1,0,0
* --noeof allows using VCF file without BGZF EOF markers. This is a very rare option to use. If your run is terminated with error message: "", then you might want to check out this option.
* --noeof allows using VCF file without BGZF EOF markers. This is a very rare option to use. If your run is terminated with error message: "", then you might want to check out this option.
==== Output Files ====
==== Output Files ====
* --prefix is optional.
* --prefix is optional.
