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--qGeno : Assigns genotype likelihood on the VCF file with fixed quality values (useful for data integration)
--qGeno : Assigns genotype likelihood on the VCF file with fixed quality values (useful for data integration)
== Subsetting
== Subsetting the VCF file ==
Suppose that you have the following index file consisting of subset of individuals in the VCF file as [subset-index]
IND_ID_1 GROUP1,GROUP2,GROUP3
IND_ID_2 GROUP2
IND_ID_3 GROUP1,GROUP3
IND_ID_4 GROUP2,GROUP3
If you run the following command:
vcfCooker --in-vcf [input-vcf-file] --out [output-prefix] --verbose --subset --in-subset [subset-index] --bgzf
Will create the following set of files
[output-prefix].GROUP1.vcf.gz
[output-prefix].GROUP2.vcf.gz
[output-prefix].GROUP3.vcf.gz
Where each VCF contains a marker polymorphic only within the group (AC>0). AC and AN fields will be updated reflecting the changes in the subset.
Additional Options Includes
--mono-subset : Includes monomorphic SNPs for the subsetting
--filt-only-subset : Use PASS-filter SNPs only for subsetting.
== Upgrading glfMultiples outputs (v 3.3 to v 4.0) ==
== Upgrading glfMultiples outputs (v 3.3 to v 4.0) ==
