Genome-wide homozygosity in Tutorial_VCF - 2 individuals affected_copy

Click on a chromosome to zoom in.

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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
434	15	37954602	40030968	n/a	n/a	region	genotypes
narrow - use this when all patients are in the same family
434	15	37954602	40030968	n/a	n/a	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 37

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 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	Tutorial_VCF	change name
analysis_name	2 individuals affected_copy	change name
max_block_length	250
max_score	434
allele_frequencies	controls
user_login	tutorial
vcf_build	37
lower_limit	0
date	2013-05-29 00:00:00
cases	Sample1,Sample2
controls	Sample3,Sample4

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