Genome-wide homozygosity in CFS2 - CFS2_fam

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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
175	7	48711437	49208360	#51957	#51973	region	genotypes
165	3	118563902	119456949	#42578	#42615	region	genotypes
150	4	15392993	16588125	#44476	#44502	region	genotypes
150	4	20818822	21752975	#44608	#44633	region	genotypes
147	4	26082689	27117580	#44741	#44762	region	genotypes
146	20	8243597	8533612	#27657	#27668	region	genotypes
142	11	2944400	3343387	#7641	#7649	region	genotypes
narrow - use this when all patients are in the same family
175	7	48711437	49208360	#51957	#51973	region	genotypes
165	3	118563902	119456949	#42578	#42615	region	genotypes
150	4	15392993	16588125	#44476	#44502	region	genotypes
150	4	20818822	21752975	#44608	#44633	region	genotypes
147	4	26082689	27117580	#44741	#44762	region	genotypes
146	20	8243597	8533612	#27657	#27668	region	genotypes
142	11	2944400	3343387	#7641	#7649	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	CFS2	change name
analysis_name	CFS2_fam	change name
max_block_length	15
max_score	175
user_login	jncldwll1
lower_limit	0
date	2013-08-08 00:00:00
cases	JC104,JC132,JC134,JC136,JC158,JC160,JC162,JC164,JC166,JC168,JC170,JC172,JC69
controls	JC252,JC254,JC256,JC258,JC261,JC267,JC269,JC271,JC273

retrieve homozyosity scores