mbiorew.blogg.se - Bam file format column

#Bam file format column how to#
#Bam file format column software#

The genotype file contains 1 line per SNP. § indiv file: see example.ind (same as above).§ snp file: see example.snp (same as above).§ genotype file: see example.eigenstratgeno.

#Bam file format column software#

This software is completely independent of our 2004 ANCESTRYMAP software.ĮIGENSTRAT Format: Used by EIGENSTRAT (both in the 07/23/06 release and in the current release). The name "ANCESTRYMAP format" is used for historical reasons only. If this entry is set to "Ignore", then that individual and all genotype data from that individual will be removed from the data set in all convertf output.

The status column might refer to Case or Control status, or might be a population group label. The gender column can be M(male), F(female) or U (unknown). The indiv file contains 1 line per individual, and has 3 columns: The genetic position can be in Morgans or centiMorgans, and the physical position is in bases. Missing genotypes are encoded by the absence of an entry in the genotype file. The genotype file contains 1 line per valid genotype, and has 3 columns:

genotype file: see example.ancestrymapgeno.

Note all the example files are in the directory:

#Bam file format column how to#

indiv file: contains information about each individualĪnd we explain how to use convertf to get from one format to another.

snp file: contains information about each SNP.

genotype file: contains genotype data for each individual at each SNP.

Note that "file format" simultaneously refers to the formats of three distinct files:

This file contains documentation of the program convertf, which converts between the 5 different file formats we support. 9.0 Input File Formats and Conversion Program