Adding fakes genotypes columns to a vcf file

Question

[xerigaj492]

Hi, I would like to know if there is any tools out there that I can use to add 4 fake samples to a VCF ?

For example for each position the first individual would have 0/0, the second would have 0/1, the third 1/0 and the last 1/1 ?

So far my plan was to do the following 4 times (one for each individuals):

grep -v "^#" MyVCF.vcf | awk '{print $0 "\t" "0|0"}'

and I would have then add the individuals names in the header manually.. but I was wondering if any of you know a better way to do it or know a tools that can do such a thing ?

Thank you !!

Answer 1

[sbstevenlee]

Not 100% sure if I understood your question, but here's a solution with Python API using the fuc package I wrote:

>>> from fuc import pyvcf
>>> data = {
...     'CHROM': ['chr1', 'chr2'],
...     'POS': [100, 101],
...     'ID': ['.', '.'],
...     'REF': ['G', 'T'],
...     'ALT': ['A', 'C'],
...     'QUAL': ['.', '.'],
...     'FILTER': ['.', '.'],
...     'INFO': ['.', '.'],
...     'FORMAT': ['GT', 'GT'],
...     'A': ['0/1', '1/1']
... }
>>> vf = pyvcf.VcfFrame.from_dict([], data)
>>> # vf = pyvcf.VcfFrame.from_file('your_vcf.vcf')
>>> vf.df
  CHROM  POS ID REF ALT QUAL FILTER INFO FORMAT    A
0  chr1  100  .   G   A    .      .    .     GT  0/1
1  chr2  101  .   T   C    .      .    .     GT  1/1
>>> vf.df['B'] = '0|0'
>>> vf.df['C'] = '0|1'
>>> vf.df['D'] = '1|0'
>>> vf.df['E'] = '1|1'
>>> vf.df
  CHROM  POS ID REF ALT QUAL FILTER INFO FORMAT    A    B    C    D    E
0  chr1  100  .   G   A    .      .    .     GT  0/1  0|0  0|1  1|0  1|1
1  chr2  101  .   T   C    .      .    .     GT  1/1  0|0  0|1  1|0  1|1
>>> vf.to_file('updated_vcf.vcf')