Genome-wide homozygosity in Canine_hom_map_27_3_12 - 300_homo_mapping_ped

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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
31	37	3902216	4045838	#242511	#127554	region	genotypes
31	37	4245875	4508283	#242532	#242548	region	genotypes
narrow - use this when all patients are in the same family
31	37	3902216	4045838	#242511	#127554	region	genotypes
31	37	4245875	4508283	#242532	#242548	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	300_homo_mapping_ped	change name
analysis_description	300 pedigree mapping
max_block_length	15
max_score	31
user_login	ahramd
homogeneity_required	homogeneity required
lower_limit	0
date	2012-03-30 00:00:00
exclusion_length	250
cases	300-007,300-008,300-032
controls	300-006

retrieve homozyosity scores