Genome-wide homozygosity in CFS2 - CFS2_fam

Click on a chromosome to zoom in.

help                tutorial

score	chr	from (bp)	to (bp)	from SNP	to SNP	build 37
broad - use this when you expect some genetic heterogeneity
120	7	48314947	48711437	#51954	#51957	region	genotypes
120	7	48711437	49208360	#51957	#51973	region	genotypes
120	7	49803375	49809742	#51979	#51981	region	genotypes
120	7	49873238	49901427	#51982	#51985	region	genotypes
120	7	49927901	49972297	#51987	#51989	region	genotypes
narrow - use this when all patients are in the same family
120	7	48314947	48711437	#51954	#51957	region	genotypes
120	7	48711437	49208360	#51957	#51973	region	genotypes
120	7	49803375	49809742	#51979	#51981	region	genotypes
120	7	49873238	49901427	#51982	#51985	region	genotypes
120	7	49927901	49972297	#51987	#51989	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	120
user_login	jncldwll1
homogeneity_required	homogeneity required
lower_limit	15
date	2013-08-08 00:00:00
exclusion_length	-1
cases	JC101,JC104,JC132,JC134,JC136,JC147,JC158,JC160,JC162,JC164,JC166,JC168,JC170,JC172,JC69
controls	JC252,JC254,JC256,JC258,JC261,JC267,JC269,JC271,JC273

retrieve homozyosity scores