Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
freebayes SNP QUAL chrishah Bioinformatics 7 05-07-2013 04:48 AM
parameter set of bwa-samtools for snp calling heiya De novo discovery 10 04-25-2012 06:27 PM
SNP phred-score threshold shuang Bioinformatics 0 08-10-2011 02:57 PM
SNP calling - is there an accepted Phred quality threshold? Francesco Lescai Bioinformatics 3 04-13-2010 11:51 AM
threshold alperyilmaz RNA Sequencing 1 02-09-2010 10:09 AM

Thread Tools
Old 07-08-2013, 06:47 AM   #1
Location: GERMANY

Join Date: Apr 2013
Posts: 16
Default how to set SNP QUAL threshold


i have created several bam files from illumina-reads (paired-end), some (3) bam-files show a coverage of around 14, some (10) bam-files with a coverage around 6. I want to use UnifiedGenotyper from GATK for SNP calling but I am unsure on how to set the QUAL threshold, as it is described to use QUAL>= 4 for coverage smaller than 10x and QUAL>=30 for a coverage of at leasat 10x. I want to do multi-sample SNPcalling with QUAL>=30, but I m not sure if I`m to hard, regarding low coverage .bams. When I use QUAL>=4 i will call several of false-positive SNPs in the high-coverage bams...

volavii is offline   Reply With Quote

coverage, quality, 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 05:13 AM.

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