Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
2nd Pass Alignment with STAR for RNA-sequencing cbaudo RNA Sequencing 3 03-04-2015 03:59 AM
Low pass filter % due to short reads eladSeq 454 Pyrosequencing 4 12-28-2012 09:32 AM
Low Pass Filter % bwking82 Illumina/Solexa 1 08-13-2009 02:23 AM

Thread Tools
Old 03-02-2020, 11:52 AM   #1
Junior Member
Location: sf bay area

Join Date: Dec 2013
Posts: 9
Default Genotyping using Low-Pass Sequencing data (0.5x - 1x)

Hi all, I am currently trying to do some genotyping using some low-pass sequencing data on 13 1000GP samples. I am mostly interested in biallelic SNPS's. I have a variant calling pipeline built on GATK 4 (HaplotypeCaller) using the best practices, and another that uses Varscan2, and another using bcftools/samtools. The idea is to produce two call sets, before and after imputation (with BEAGLE) and check concordance with imputed 1000GP truth sets. Would any of you have suggestions on the best approach here? HaplotypeCaller may not be the best choice if there are only a few or one read is my thought. Any suggestions are appreciated! -Karl
karl_s is offline   Reply With Quote

genotyping, low-pass, snp analysis

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 05:12 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO