Changes

'''Option 2'''

'''Option 2'''

Alternatively, if you want to refine the variant and genotype calling using family relatedness based on your existing VCF files, polymutt can take a VCF file as input. In this case, the VCF file has to have the PL or the GL field, which is usually available from commonly used tools (e.g. GATK and samtools).

Alternatively, if you want to refine the variant and genotype calling using family relatedness based on your existing VCF files, polymutt can take a VCF file as input. In this case, the VCF file has to have the PL or the GL field, which is usually available from commonly used tools (e.g. GATK and samtools).

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).

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).