merging two VCF files

Question

[Zahra]

Hi all,

I have two VCF files (Indel and SNV), and when I wanted to merge them by the gatk tool, I received the error:

“A sequence dictionary must be available”

so I tried to use UpdateVCFSequenceDictionary and hg19 dictionary, then I faced a new error:

“Key SNP found in VariantContext field INFO at chr1:548426 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default”

and now I do not know how to solve this problem.

Would you mind helping me, please?

Answer 1

[Pierre Lindenbaum]

see Key DP found in VariantContext field FILTER error and SortVCF in Picard

[Zahra]

Thanks a lot

Answer 2

[sbstevenlee]

Check out the fuc Python package I wrote:

For command line interface (CLI):

$ fuc vcf_merge 1.vcf 2.vcf 3.vcf > merged.vcf

For application programming interface (API):

Assume we have the following data:

>>> from fuc import pyvcf
>>> data1 = {
...     'CHROM': ['chr1', 'chr1'],
...     'POS': [100, 101],
...     'ID': ['.', '.'],
...     'REF': ['G', 'T'],
...     'ALT': ['A', 'C'],
...     'QUAL': ['.', '.'],
...     'FILTER': ['.', '.'],
...     'INFO': ['.', '.'],
...     'FORMAT': ['GT:DP', 'GT:DP'],
...     'Steven': ['0/0:32', '0/1:29'],
...     'Sara': ['0/1:24', '1/1:30'],
... }
>>> data2 = {
...     'CHROM': ['chr1', 'chr1', 'chr2'],
...     'POS': [100, 101, 200],
...     'ID': ['.', '.', '.'],
...     'REF': ['G', 'T', 'A'],
...     'ALT': ['A', 'C', 'T'],
...     'QUAL': ['.', '.', '.'],
...     'FILTER': ['.', '.', '.'],
...     'INFO': ['.', '.', '.'],
...     'FORMAT': ['GT:DP', 'GT:DP', 'GT:DP'],
...     'Dona': ['./.:.', '0/0:24', '0/0:26'],
...     'Michel': ['0/1:24', '0/1:31', '0/1:26'],
... }
>>> vf1 = pyvcf.VcfFrame.from_dict([], data1)
>>> vf2 = pyvcf.VcfFrame.from_dict([], data2)
>>> vf1.df
  CHROM  POS ID REF ALT QUAL FILTER INFO FORMAT  Steven    Sara
0  chr1  100  .   G   A    .      .    .  GT:DP  0/0:32  0/1:24
1  chr1  101  .   T   C    .      .    .  GT:DP  0/1:29  1/1:30
>>> vf2.df
  CHROM  POS ID REF ALT QUAL FILTER INFO FORMAT    Dona  Michel
0  chr1  100  .   G   A    .      .    .  GT:DP   ./.:.  0/1:24
1  chr1  101  .   T   C    .      .    .  GT:DP  0/0:24  0/1:31
2  chr2  200  .   A   T    .      .    .  GT:DP  0/0:26  0/1:26

We can merge the two VcfFrames with how='inner' (default):

>>> pyvcf.merge([vf1, vf2]).df
  CHROM  POS ID REF ALT QUAL FILTER INFO FORMAT Steven Sara Dona Michel
0  chr1  100  .   G   A    .      .    .     GT    0/0  0/1  ./.    0/1
1  chr1  101  .   T   C    .      .    .     GT    0/1  1/1  0/0    0/1

We can also merge with how='outer':

>>> pyvcf.merge([vf1, vf2], how='outer').df
  CHROM  POS ID REF ALT QUAL FILTER INFO FORMAT Steven Sara Dona Michel
0  chr1  100  .   G   A    .      .    .     GT    0/0  0/1  ./.    0/1
1  chr1  101  .   T   C    .      .    .     GT    0/1  1/1  0/0    0/1
2  chr2  200  .   A   T    .      .    .     GT    ./.  ./.  0/0    0/1

Since both VcfFrames have the DP subfield, we can use format='GT:DP':

>>> pyvcf.merge([vf1, vf2], how='outer', format='GT:DP').df
  CHROM  POS ID REF ALT QUAL FILTER INFO FORMAT  Steven    Sara    Dona  Michel
0  chr1  100  .   G   A    .      .    .  GT:DP  0/0:32  0/1:24   ./.:.  0/1:24
1  chr1  101  .   T   C    .      .    .  GT:DP  0/1:29  1/1:30  0/0:24  0/1:31
2  chr2  200  .   A   T    .      .    .  GT:DP   ./.:.   ./.:.  0/0:26  0/1:26