2,004
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Input Files
==== PED and DAT Files ====
==== PED and DAT Files ====
* When PED file has genotypes saved, there is no need for a VCF file as input.
* When PED file has genotypes saved, there is no need for a VCF file as input.
* Rare-Metal-Worker takes PED/DAT file in Merlin format. Please refer here [[http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html]] for details.
* Rare-Metal-Worker takes PED/DAT file in Merlin format. Please refer here [[http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html | PED/DAT format description]] for details.
* DAT file must have variant names in the following format "M chr:pos". Here is an example of variant name format in DAT file:
* DAT file must have variant names in the following format "M chr:pos". Here is an example of variant name format in DAT file:
M 1:123456
M 1:123456
==== VCF File ====
==== VCF File ====
* Another option is to use VCF as input. Please refer to the following link for VCF file specification: [[http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41]]
* Another option is to use VCF as input. Please refer to the following link for VCF file specification: [[http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 | 1000 genome wiki VCF specs]]
* VCF file should be compressed by bgzip and indexed by tabix, using the following command:
* VCF file should be compressed by bgzip and indexed by tabix, using the following command:
bgzip input.vcf ## this command will produce input.vcf.gz
bgzip input.vcf ## this command will produce input.vcf.gz
