Genome-wide homozygosity in Tutorial - tutorial

Click on a chromosome to zoom in.

help                tutorial

score	chr	from (bp)	to (bp)	from SNP	to SNP	build 36
broad - use this when you expect some genetic heterogeneity
400	7	29752907	36514214	rs850126	rs3911827	region	genotypes
narrow - use this when all patients are in the same family
400	7	29911394	36309112	rs10488082	rs196628	region	genotypes
325	7	36309112	36514214	rs196628	rs3911827	region	genotypes
321	7	29801545	29852469	rs6971564	rs174941	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

call GeneDistiller build 36

with all narrow broad regions at once

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 36
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	Tutorial	change name
analysis_name	tutorial	change name
max_block_length	80
max_score	400
allele_frequencies	controls
user_login	tutorial
cases	NA06993,NA07019,NA07034,NA07056,NA07357
controls	NA10835,NA10846,NA10854

retrieve homozyosity scores
new & highly experimental: show this for build 36