Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Consensus Calling BCFTOOLS PacBio gaps uloeber Bioinformatics 2 07-27-2017 03:18 AM
Why MAQ consensus seq better than SAMtools consensus ?? av_d Genomic Resequencing 5 10-18-2015 04:44 AM
consensus sequence with samtools and bcftools 1.2 popo Bioinformatics 0 02-16-2015 10:44 AM
bcftools consensus from BCF/VCF rwhet052 Bioinformatics 1 02-04-2015 06:03 AM
Differences in Consensus Sequences bhan Genomic Resequencing 0 08-01-2011 08:36 AM

Thread Tools
Old 08-08-2018, 02:58 AM   #1
Junior Member
Location: netherlands

Join Date: Nov 2017
Posts: 3
Smile bcftools consensus: shorter consensus sequences

Hi all,
I am trying to get the consensus sequences for chloroplast genomes using a reference. Here are my command lines:
~/samtools-1.3/samtools mpileup -Ou -f REF alnsorted.bam | bcftools call -mv -Oz -o 1aln_paired.vcf.gz 

tabix aln_paired.vcf.gz

cat REF | bcftools consensus aln_paired.vcf.gz > consensus_paired.fa
I am getting shorter consensus sequences, my reference is 159.295 bp long and for each constructed genome I get around 158.700 158.900 bp. I have checked the vcf file and there are a lot of deletions. Is this something that can happen or I am using some wrong settings in my codes?

thanks a lot in advance
ireneirene is offline   Reply With Quote
Old 08-08-2018, 09:13 PM   #2
Location: Europe

Join Date: Oct 2016
Posts: 55


why you crossposted this here on seqanswer, if you already get an answer/guess in biostars.

If this answer isn't enough for you please give feedback there.

fin swimmer
finswimmer is offline   Reply With Quote

bcftools read mapping

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 08:45 PM.

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