Extracting this data frame from a .vcf file

Question

[zizigolu]

Hi,

I have one .vcf file of whole genome sequencing of tumour Vs normal samples of 21 patients.

I need a data from like this as input for a tool for finding driver genes

> head(mutations)
  sampleID chr      pos ref mut
1 Sample_1   1   871244   G   C
2 Sample_1   1  6648841   C   G
3 Sample_1   1 17557072   G   A
4 Sample_1   1 22838492   G   C
5 Sample_1   1 27097733   G   A
6 Sample_1   1 27333206   G   A

In separated .vcf files for each patient I have start, end, chromosome, ref, and variant allele. However I am sure how to get such data frame from this big vcf

Any help please?

Thank you

[zx8754]

This is a basic question, please invest some time to read through bcftools manuals. Or if you choose to stay in R, then read about vcfR package.

[zizigolu]

Thank you I also tried vcfR

> read.vcfR("trg.snp.pass.vcf")
Error in read.vcfR("trg.snp.pass.vcf") : 
  File: trg.snp.pass.vcf does not appear to be a VCF file.
  First line of file:
 trg.snp.pass.vcf 
  Should begin with:
##fileformat=VCFv 
In addition: Warning message:
In scan(file = file, what = character(), nmax = 1, sep = "\n", quiet = TRUE,  :
  embedded nul(s) found in input
> read.vcfR("trg.snp.pass.vcf.tar")
Error in read.vcfR("trg.snp.pass.vcf.tar") : 
  File: trg.snp.pass.vcf.tar does not appear to be a VCF file.
  First line of file:
 trg.snp.pass.vcf.tar 
  Should begin with:
##fileformat=VCFv 
In addition: Warning message:
In scan(file = file, what = character(), nmax = 1, sep = "\n", quiet = TRUE,  :
  embedded nul(s) found in input
>

[zizigolu]

bcftools query plugin and snpsift plugin in galaxy also do that

Answer 1

[zx8754]

Using bcftools:

bcftools query -f '[%SAMPLE %CHROM %POS %REF %ALT %GT\n]' myFile.vcf > myFileLong.txt

[zizigolu]

Thank you,

says

[fi1d18@cyan01 ~]$ [fi1d18@cyan01 ~]$ bcftools query -f '[%SAMPLE %CHROM %POS %REF %ALT %GT\n]' trg.snp.pass.vcf > myFileLong.txt
-bash: [fi1d18@cyan01: command not found
[fi1d18@cyan01 ~]$ Failed to open trg.snp.pass.vcf: unknown file type

And when I tried for .vcf for one sample says

[fi1d18@cyan01 ~]$ [fi1d18@cyan01 ~]$ bcftools query -f '[%SAMPLE %CHROM %POS %REF %ALT %GT\n]' LP2000104-DNA_A01_vs_LP2000101-DNA_A01.passed.somatic.indel.vcf > myFileLong.txt
bash: [fi1d18@cyan01: command not found
[fi1d18@cyan01 ~]$ Error: no such tag defined in the VCF header: FORMAT/GT

[finswimmer]

bash: [fi1d18@cyan01: command not found

Your command line doesn't start with bcftools. The first thing that is trying to start is [fi1d18@cyan01. Make sure there are no more symbols before the command you like to start.

fin swimmer

[GenoMax]

Either provide full path for bcftools or add the directory with that executable to your $PATH. export PATH=$PATH:/dir_for_bcftools

[zizigolu]

Sorry, I am in path but either galaxy or in Linux I am getting this error

Error: no such tag defined in the VCF header: FORMAT/GT

and galaxy says

Fatal error: Exit code 255 ()
Error: no such tag defined in the VCF header: INFO/REFt. FORMAT fields must be in square brackets, e.g. "[ REFt]"

The head of my vcf is this

##bcftools_viewCommand=view -h c.vcf
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NORMAL  TUMOR

I don't know what is going wrong in my vcf files though

[finswimmer]

Are you sure that this is the complete header?

bcftools is very strict about the vcf specs. So the first line must be:

##fileformat=VCFv4.1

(Version number can differ)

For each contig you need an entry like this:

##contig=<ID=chr1,length=248956422>

For each key in the INFO and FORMAT column you need in entry in the header. For GT this looks like this:

##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">

So, are there more entry in the header?

fin swimmer

Answer 2

[zizigolu]

bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%ID]\n' c.vcf

This solve the error

bcftools query plugin and snpsift plugin in galaxy also do that

[zx8754]

Great it worked out, accept it if this was the solution.

[zizigolu]

%END would return the start and end

Answer 3

[andrew.j.skelton73]

GATK has a tool for that, see VariantsToTable