Hi,

I have been trying to use samtools to create consensus sequences. However, it seems that conseqs.fastq (see command below) is missing consensus sequences for most reference sequences.

--- samtools command ---
samtools mpileup -uf ref.fa sorted.bam | bcftools view -cg - | /usr/share/samtools/vcfutils.pl vcf2fq > conseqs.fastq
----

In IGV, I can create consensus sequence for all references (one by one). I would like to create the consensus sequences with a command line tool.

I asked this question at seqanswers forum and got an answer that creating the consensus sequences is possible with UGENE command line.

Can I have an example of an UGENE command that can be used to build consensus sequences from ref.fasta and sorted.bam files?

Thanks

Hello,

In the current UGENE version 1.14.1 you can do the task only partially:

1) You can find out variants by a reference sequence and an assembly. It is the same as command:

Code:

samtools mpileup –uf <input_reference> <input_bam> | bcftools view –vg – | vcfutils.pl varFilter –D 100

For details, see: Call Variants with SAMtools

2) You can find out a consensus sequence from an assembly.
For details, see: Extract Consensus from Assembly

Unfortunately, it is not possible to get a new sequence from a reference + variations combination. We will add this feature into the next major UGENE release 1.15. Here is the link to the corresponding request in our issue-tracking system: UGENE-3588
Note that any workflow in UGENE can also be run from the command line.

Is the input still the same to do this in version 1.15 because I input that code and nothing happened.

Quote:

Is the input still the same to do this in version 1.15 because I input that code and nothing happened.

What do you mean? The workflow in UGENE is still the same. Do you mean the original SAMtools command line tool?

Question: What Better Way To Get Consensus Sequence Of Mapping Against Reference Genome Using Samtools Mpileup?
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You can see the members area ADELE WEIGHT LOSS .

I'm still using version 1.14.1 because I love this version so much that I never updated it. But I can't get a new sequence from a reference and variations combination in this version. What do you suggest? Should I upgrade to the latest version 1.29.0? Or is it possible to do so in any version above 1.14.1? If yes, where can I download it from?

Priscilla Hamer wrote on May 22^nd, 2018 at 7:02am:

I'm still using version 1.14.1 because I love this version so much that I never updated it. But I can't get a new sequence from a reference and variations combination in this version. What do you suggest? Should I upgrade to the latest version 1.29.0? Or is it possible to do so in any version above 1.14.1? If yes, where can I download it from?

Thank you for the feedback, Priscilla!

Unfortunately, this feature is not yet available in UGENE 1.29.0 as well. Instead, you might use, for example, FastaAlternateReferenceMaker from GATK (in the command line).

We'll take into account your request and add this feature in one of the nearest UGENE versions.

I also use the version UGENE 1.14.1. And this version perfectly works  for me. Is there any updated version?

Hi lexen luis!

Yes, current UGENE version is 1.30. See a brief description of new features here: http://ugene.net/changelist.html.

Priscilla Hamer wrote on May 22^nd, 2018 at 7:02am:

I'm still using version 1.14.1 because I love this version so much that I never updated it. But I can't get a new sequence from a reference and variations combination in this version. What do you suggest? Should I upgrade to the latest version 1.29.0? Or is it possible to do so in any version above 1.14.1? If yes, where can I download it from?

lexen luis wrote on Jun 25^th, 2018 at 2:55pm:

I also use the version UGENE 1.14.1. And this version perfectly works  for me. Is there any updated version?

The UGENe has many updates after this the current stable version is 1.31.0 (August, 2018).

Hello there you can do it in the current UGENE version 1.14.1 you can do the task only partially

Peyton12345 wrote on Aug 28^th, 2018 at 9:33pm:

Hello there you can do it in the current UGENE version 1.14.1 you can do the task only partially

Thank for the help it would be really appreciable. :)

is the input same of the version when ever i input something nothing happens

Peytonn james wrote on Aug 29^th, 2018 at 8:35pm:

is the input same of the version when ever i input something nothing happens

Are you using the latest version (1.31.1)? Because it is working fine for me.

Duncan David wrote on Dec 7^th, 2018 at 9:08am:

Peytonn james wrote on Aug 29th, 2018 at 8:35pm: is the input same of the version when ever i input something nothing happens Are you using the latest version (1.31.1)? Because it is working fine for me.

yes, I check this version. It's definitely work fine for me

Peytonn james wrote on Aug 29^th, 2018 at 8:35pm:

is the input same of the version when ever i input something nothing happens

Yes, you are right. it is the same version.