Question: Error in SNP calling, samtools
1
gravatar for Adrian Pelin
3.9 years ago by
Adrian Pelin2.1k
Canada
Adrian Pelin2.1k wrote:

Hello,

 

I have been following what most tutorials are suggesting (https://wikis.utexas.edu/display/bioiteam/Variant+calling+using+SAMtools), and I get:

@NCS ~/heterozygosity/TrimReads/bwa_Mapping_9iso_REF_GDR18/vcf/samtools_diploid $ samtools mpileup -uf gdr18_k75-85_NHC_conc.fasta ../../GDR-18.sort.grp.md.bam | bcftools view -vcg - > GDR18.vcf
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
[E::cg] unknown type

The first part executed without a problem and I can generate a .bcf file, it's the second part (bcftools) that gives an error for some reason.

Adrian

 

EDIT:

Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)
Version: 0.2.0-rc9-29-gfcd7b41 (using htslib 0.2.0-rc9-20-gb7c2a46)

Program: samtools (Tools for alignments in the SAM format)
Version: 0.2.0-rc9-11-g5ec815e (using htslib 0.2.0-rc9-20-gb7c2a46)

 

snp bcftools ngs vcf • 4.5k views
ADD COMMENTlink modified 2.5 years ago by vassialk150 • written 3.9 years ago by Adrian Pelin2.1k

Which version of samtools and bcftools are you using?
 

ADD REPLYlink written 3.9 years ago by Devon Ryan79k

Sorry I didn't immediately add those, but I added that information into the original post after EDIT.

ADD REPLYlink written 3.9 years ago by Adrian Pelin2.1k

Try using the release version instead of the development version.

ADD REPLYlink written 3.9 years ago by Devon Ryan79k

Thanks, worked!

mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
[bcfview] 100000 sites processed.
[afs] 0:71676.849 1:28170.018 2:153.133
[bcfview] 200000 sites processed.
[afs] 0:74382.499 1:25350.294 2:267.207
[bcfview] 300000 sites processed.
[afs] 0:78517.541 1:20777.378 2:705.081
[afs] 0:37420.685 1:6159.299 2:823.016

 

ADD REPLYlink written 3.9 years ago by Adrian Pelin2.1k

Hi Adrian,

I have the same problem as you posted. You have figured out the error. Could you give me some help about this?

Best

ZQ

ADD REPLYlink written 3.0 years ago by wu.zhiqiang.102020

I used the version by Devon Ryan . But the error is still here. Please help

ZQ

ADD REPLYlink written 3.0 years ago by wu.zhiqiang.102020

Hi,

I'm also having a similar problem, but I am not using the development version of sam/bcftools. So;

 

samtools mpileup -d8000 -IEuf hg19.fa input.bam | bcftools view -vg - > output.vcf

 

Gives the message;

 

[mpileup] 1 samples in 1 input files

[E::g] unknown type

 

Do you know what is happening here? I'm using;

 

samtools 1.1, htslib 1.1

bcftools 1.1, htslib 1.1

 

Thank you,

Callum

 

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by Callum0
1

I think the guide is for older version of samtools, so some of the options you are using are likely obsolete.

Not sure where you can an updated guide.

ADD REPLYlink written 3.6 years ago by Adrian Pelin2.1k

I'm getting the same error using versions 1.1, did you have any luck finding a solution?

ADD REPLYlink written 3.5 years ago by klarke20

The error was actually related to the options for the command "bcftools view -bvcg". It was expecting additional parameters after the flags.

type bcftools view to read the doc and decide what you need, if anything

ADD REPLYlink written 3.5 years ago by Ed Simpson0
0
gravatar for vassialk
2.5 years ago by
vassialk150
Belarus
vassialk150 wrote:

Try the other reliable software like NextGene, CLC, GenPro.... Command line tools lack quality rather often... and have not enough robustness and test experience....

ADD COMMENTlink written 2.5 years ago by vassialk150
2

I'm sorry, but that's utter nonsense. NextGene, CLC, and such are all inflexible, GUI based suites that lack reproducibility and the ability to do anything other than the vanilla approaches to data analysis. Command line tools are much more flexible, and open to you tailoring them to your experimental design. 

ADD REPLYlink written 2.5 years ago by andrew.j.skelton734.8k

I hope this is a joke.

ADD REPLYlink written 2.5 years ago by Devon Ryan79k

Please stay on topic.

ADD REPLYlink written 2.5 years ago by Michael Dondrup44k

Maybe a NextGen troll.

ADD REPLYlink written 2.5 years ago by Michael Dondrup44k
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