Error in SNP calling, samtools

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)

ngs bcftools vcf snp

• 8,290 views • link

updated 4.8 years ago by Ram

• written 12.1 years ago by Adrian Pelin

Which version of samtools and bcftools are you using?

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updated 6.7 years ago by Ram

• written 12.1 years ago by Devon Ryan

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

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updated 4.8 years ago by Ram

• written 12.1 years ago by Adrian Pelin

Try using the release version instead of the development version.

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updated 4.8 years ago by Ram

• written 12.1 years ago by Devon Ryan

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

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updated 6.7 years ago by Ram

• written 12.1 years ago by Adrian Pelin

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

• 1 views • link

updated 4.8 years ago by Ram

• written 11.2 years ago by wu.zhiqiang.1020 •

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

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updated 4.8 years ago by Ram

• written 11.2 years ago by wu.zhiqiang.1020 •

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

• 0 views • link

updated 6.7 years ago by Ram

• written 11.8 years ago by Callum •

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.

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updated 4.8 years ago by Ram

• written 11.8 years ago by Adrian Pelin

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

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updated 4.8 years ago by Ram

• written 11.7 years ago by klarke2 •

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

• 0 views • link

updated 4.8 years ago by Ram

• written 11.7 years ago by Ed Simpson •

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