5
$\begingroup$

I have VCF files (SNPs & indels) for WGS on 100 samples, but I want to only use a specific subset of 10 of the samples. Is there a relatively easy way to pull out only the 10 samples, while still keeping all of the data for the entire genome?

I have a script that allows me to pull out regions of the whole genome for all 100 samples, so if I could do something similar but only put regions for the 10 samples that I want that would be ideal.

Thanks for the help!

$\endgroup$
  • 1
    $\begingroup$ Welcome. Do you want random 10 samples or do you want to extract specific 10 samples? Also, do you talk about vcf files containing SNPs/indels ? What is the reason why you want to subsample your vcf file? We like details, details make questions understandable and answerable. You can edit your Q and add all the details. $\endgroup$ – Kamil S Jaron Feb 7 '18 at 16:08
6
$\begingroup$

Bcftools has sample/individual filtering as an option for most of the commands. You can subset individuals by using the -s or -S option:

-s, --samples [^]LIST

Comma-separated list of samples to include or exclude if prefixed with "^". Note that in general tags such as INFO/AC, INFO/AN, etc are not updated to correspond to the subset samples. bcftools view is the exception where some tags will be updated (unless the -I, --no-update option is used; see bcftools view documentation). To use updated tags for the subset in another command one can pipe from view into that command. For example:

-S, --samples-file FILE

File of sample names to include or exclude if prefixed with "^". One sample per line. See also the note above for the -s, --samples option. The command bcftools call accepts an optional second column indicating ploidy (0, 1 or 2) or sex (as defined by --ploidy, for example "F" or "M"), and can parse also PED files. If the second column is not present, the sex "F" is assumed. With bcftools call -C trio, PED file is expected. File formats examples:

sample1    1
sample2    2
sample3    2

or

sample1    M
sample2    F
sample3    F

or a .ped file (here is shown a minimum working example, the first column is ignored and the last indicates sex: 1=male, 2=female):

ignored daughterA fatherA motherA 2
ignored sonB fatherB motherB 1

Example usage:

bcftools view -s sample1,sample2 file.vcf > filtered.vcf
bcftools view -S sample_file.txt file.vcf > filtered.vcf

See the bcftools manpage for more information.

| improve this answer | |
$\endgroup$
1
$\begingroup$

You can use the GATK's SelectVariants tool with the -sn flag.

E.g.

gatk SelectVariants -V input.vcf -R reference.fasta -sn Sample_01 -out sample.vcf

You may use the -sn flag several times so as to select several samples, or use it to point to a file containing a sample name on every line.

| improve this answer | |
$\endgroup$
1
$\begingroup$

In addition to the answer from @gringer there is a bcftools plugin called split that can do this, but gives you the added ability to output single-sample VCFs by specifying a filename for each sample.

$ bcftools +split

About: Split VCF by sample, creating single-sample VCFs.

Usage: bcftools +split [Options]
Plugin options:
   -e, --exclude EXPR              exclude sites for which the expression is true (applied on the outputs)
   -i, --include EXPR              include only sites for which the expression is true (applied on the outputs)
   -k, --keep-tags LIST            list of tags to keep. By default all tags are preserved
   -o, --output DIR                write output to the directory DIR
   -O, --output-type b|u|z|v       b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]
   -r, --regions REGION            restrict to comma-separated list of regions
   -R, --regions-file FILE         restrict to regions listed in a file
   -S, --samples-file FILE         list of samples to keep with second (optional) column for basename of the new file
   -t, --targets REGION            similar to -r but streams rather than index-jumps
   -T, --targets-file FILE         similar to -R but streams rather than index-jumps
Examples:
   # Split a VCF file
   bcftools +split input.bcf -Ob -o dir

   # Exclude sites with missing or hom-ref genotypes
   bcftools +split input.bcf -Ob -o dir -i'GT="alt"'

   # Keep all INFO tags but only GT and PL in FORMAT
   bcftools +split input.bcf -Ob -o dir -k INFO,FMT/GT,PL

   # Keep all FORMAT tags but drop all INFO tags
   bcftools +split input.bcf -Ob -o dir -k FMT

So if you had the following samples file samples.tsv

sample1    sample1
sample2    sample2

You can run it and get the following

$ bcftools +split -S samples.tsv -o outdir in.vcf
$ ls
in.vcf sample1.vcf sample2.vcf

Without the second column, you would just get a single VCF with the two samples in it (as you would with view)

| improve this answer | |
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.