Go Back   SEQanswers > Sequencing Technologies/Companies > MGISEQ (FKA Complete Genomics)

Similar Threads
Thread Thread Starter Forum Replies Last Post
Gene prediction algorithms for humans Heena Farooq 454 Pyrosequencing 3 08-14-2015 08:33 AM
mpileup and homozygous snps grievous Bioinformatics 5 02-19-2014 05:58 PM
Pathogenic bacteria against humans santi.ontanon Bioinformatics 3 07-15-2013 01:47 PM
homozygous and heterozygos asankaf General 15 04-04-2013 03:03 PM
GATK, Homozygous Ref and GQ etorstenson Bioinformatics 0 08-09-2012 11:11 AM

Thread Tools
Old 07-29-2017, 03:14 PM   #1
Junior Member
Location: United states

Join Date: Jul 2017
Posts: 2
Lightbulb Hetrozygous / Homozygous variant ratio humans

Hi everyone,

Does anyone have an idea what the het/hom variant ratio is for humans?

Is 0.7-1 reasonable depending on population for WGS

For example, here is what I got with my GATK pipeline:

Sample 1 (E European)

1- After BQSR- 1.03
2- After HaplotypeCaller- 0.73
3- After VQSR- 0.72

Sample 2 (Siberian):

1- After BQSR- 1.32
2- After HaplotypeCaller- 1.0
3- After VQSR - 0.99

Just trying to gauge whether my filtering is too aggressive and that I am filtering out too many true positive SNPs.

With regards to novel SNPs:

Sample 1:
1- After BQSR- 10%
2- After VQSR- 1%

Sample 2:

Same as sample 1
Ghani is offline   Reply With Quote

bqsr, vqsr

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 09:12 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO