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[[Category:Software|vcfCooker]]
[[Category:Software|vcfCooker]]
(Updated at 2012/01/20 10:47PM)
'''vcfCooker''' is a software that converts VCF/BED file formats in various forms. vcfCooker is currently under development, and will be publicly released soon. The current documentation contains the minimal information of currently working functions.
'''vcfCooker''' is a software that converts VCF/BED file formats in various forms. vcfCooker is currently under development, and will be publicly released soon. The current documentation contains the minimal information of currently working functions.
--maxABZ [2147483647],
--maxABZ [2147483647],
--maxBCS [2147483647], --keepFilter
--maxBCS [2147483647], --keepFilter
== Converting between VCF/PLINK file format ==
In order to convert from VCF to PLINK (binary PED) format, use the following command
vcfCooker --in-vcf [input-vcf-file] --out [output-bfile] --write-bed --verbose
This command will convert the file to PLINK format. It will work correctly only on biallelic SNPs.
In order to convert from PLINK (binary PED) format to VCF format, use the following command
vcfCooker --in-bfile [input-bfile] --out [output-vcf] --write-vcf --bgzf --verbose
This command will convert PLINK format into VCF format, matching the reference sequence assuming forward strand by default. More specifically
* If either of the two alleles matches with reference allele, it assumes forward strand and determine REF/ALT
* Otherwise, it try to see if strand flipping make either allele match to the reference allele. if it does, it flips the strand and determine REF/ALT
Additional Options Includes
--ref [/data/local/ref/karma.ref/human.g1k.v37.fa] : To change the genome reference sequence to compare against
--qGeno : Assigns genotype likelihood on the VCF file with fixed quality values (useful for data integration)
== Subsetting
== Upgrading glfMultiples outputs (v 3.3 to v 4.0) ==
== Upgrading glfMultiples outputs (v 3.3 to v 4.0) ==
