Genome-wide homozygosity in Canine_hom_map_27_3_12 - 320_ped_homo_mapping

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score	chr	from (bp)	to (bp)	from SNP	to SNP	build 37
broad - use this when you expect some genetic heterogeneity
102	19	3103155	4340151	#200144	#200208	region	genotypes
narrow - use this when all patients are in the same family
102	19	3103155	4340151	#200144	#200208	region	genotypes

change threshold

0.99 x max 0.9 x max 0.8 x max 0.7 x max 0.6 x max 0.5 x max

create files for Alohomora
flanking region [bp] allele frequencies from all samples allele frequencies from controls allele frequencies equally distributed narrow regions broad regions

create a BED file build 37
complete homozygous regions shown here		narrow regions broad regions
complete genes within these only exons	flanked by bases on each side.

analysis settings
project_name	Canine_hom_map_27_3_12	change name
analysis_name	320_ped_homo_mapping	change name
analysis_description	analysis of 320 pedigree members homoz mzpping_7
max_block_length	80
max_score	102
user_login	ahramd
homogeneity_required	homogeneity required
lower_limit	0
date	2012-03-29 00:00:00
exclusion_length	1000
cases	320-001,320-003,320-005
controls	320-006,320-007,320-008,350-004

retrieve homozyosity scores