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* If some of the members are not sequenced but are in the pedigree because of the relatedness with other members, the GLF_Index column (6th column) in the ped file should be set to zero
* If some of the members are not sequenced but are in the pedigree because of the relatedness with other members, the GLF_Index column (6th column) in the ped file should be set to zero
* For unrelated individuals, you can either (1) create a family for each unrelated individual as a founder or (2) put all unrelated individuals as founders in a single family.
* For unrelated individuals, you can either (1) create a family for each unrelated individual as a founder or (2) put all unrelated individuals as founders in a single family.
* See "examples" in the downlaod for more info.
'''Option 2'''
'''Option 2'''
''NOTE'': this options does not work for de novo mutation detection in this version due to the lack of sequencing information in most VCF files.
''NOTE'': this options does not work for de novo mutation detection in this version due to the lack of sequencing information in most VCF files.
In this option, you can specify --in_vcf input.vcf in place of -g input.gif for variant calling. If both the --in_vcf ang -g options are specified, --in_vcf will take action while -g will not. The .ped and .dat files are as in Option 1 but only first 5 columns are in effect and other columns will be ignored. You can remove the GLF_Index column but currently it still require the presence of .dat file even if it is empty.
In this option, you can specify --in_vcf input.vcf in place of -g input.gif for variant calling. If both the --in_vcf ang -g options are specified, --in_vcf will take action while -g will not. The .ped and .dat files are as in Option 1 but only first 5 columns are in effect and other columns will be ignored. You can remove the GLF_Index column but currently it still requires the presence of .dat file even if it is empty (will make it more flexible in future versions).
*See "examples" in the downlaod for more info.
== Other options ==
== Other options ==
