SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Transcriptome assembly: Low GC, short contigs, low read alignment jmah Bioinformatics 0 03-15-2017 04:47 PM
Low intensity & quality for Index Read 2 kmcarr Illumina/Solexa 5 09-29-2016 02:16 AM
Low quality in the middle of the read? MG1655 Illumina/Solexa 0 08-12-2012 12:22 PM
Read Depth in vcf (samtools / bcftools) Marie_Noir Bioinformatics 1 04-17-2012 06:48 AM
Periodical illumina read length distribution after trimming of low-quality bases luxmare General 4 12-20-2010 03:18 PM

Reply
 
Thread Tools
Old 05-17-2018, 03:42 PM   #1
clintp
Member
 
Location: Georgia

Join Date: Apr 2013
Posts: 19
Default bcftools - retain low quality read position support?

Is it possible to have `bcftools call -c` output a DP4 values that add up to the total DP value. I want to call simple consensus sequences based on a basic vote.

For example, at one position in my VCF file, I have:
DP=16092 and DP4=74,48,24,600 (alt allele should win 624 to 122)
Those dont come close to adding up.
Checking out the position in IGV, the ref allele wins 11355 to 3716.

I did run samtools mpileup -B to turn off BAQ scoring.
What am I missing here?
clintp is offline   Reply With Quote
Reply

Tags
analysis, bcftools, bioinformatic tools, samtools

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 08:31 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO