How to merge vcf files with different variants but same samples?

Question

[humeira.tayyab]

I have vcf files with exactly same meta region as well as same column names for fix and gt region but different variants. I want to merge them into a single file vcf file with same meta and combined fixed and gt region.like this :

file1.vcf

 ##fileformat=VCFv4.1 
 ##FILTER=<ID=PASS,Description="Passed all filters">
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Read Depth">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 #CHROM POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  S1  S2  S3
1   10  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/1 0/0 0/1
1   11  .   C   A   .   .   DP=3;CALLER=Samtools    GT  .   .   1/1
1   12  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/0 0/0 0/0
1   13  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/1 1/1 1/1

file2.vcf

  ##fileformat=VCFv4.1
  ##FILTER=<ID=PASS,Description="Passed all filters">  
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Read Depth">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 #CHROM POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  S1  S2  S3
1   14  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/1 0/0 0/1
1   15  .   C   A   .   .   DP=3;CALLER=Samtools    GT  .   .   1/1
1   16  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/0 0/0 0/0
1   17  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/1 1/1 1/1

merged.vcf

 ##fileformat=VCFv4.1
 ##FILTER=<ID=PASS,Description="Passed all filters">
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Read Depth">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 #CHROM POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  S1  S2  S3
1   10  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/1 0/0 0/1
1   11  .   C   A   .   .   DP=3;CALLER=Samtools    GT  .   .   1/1
1   12  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/0 0/0 0/0
1   13  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/1 1/1 1/1
1   14  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/1 0/0 0/1
1   15  .   C   A   .   .   DP=3;CALLER=Samtools    GT  .   .   1/1
1   16  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/0 0/0 0/0
1   17  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/1 1/1 1/1

[Ram]

What have you tried? Have you checked vcftools/bcftools? Also, please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Answer 1

[Kevin Blighe]

Just use bcftools concat. You should additionally get into the habit of normalising your VCF files prior to performing downstream analyses on them. This can be done with bcftools norm -m-any (I have not done that for the purposes of this answer):

bgzip file1.vcf
bgzip file2.vcf

tabix -p file1.vcf.gz
tabix -p file2.vcf.gz
bcftools concat file1.vcf.gz file2.vcf.gz 

##fileformat=VCFv4.1 
##FILTER=<ID=PASS,Description="All filters passed">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Read Depth">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=1>
##bcftools_concatVersion=1.2+htslib-1.2.1
##bcftools_concatCommand=concat file1.vcf.gz file2.vcf.gz
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  S1  S2  S3
1   10  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/1 0/0 0/1
1   11  .   C   A   .   .   DP=3;CALLER=Samtools    GT  .   .   1/1
1   12  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/0 0/0 0/0
1   13  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/1 1/1 1/1
1   14  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/1 0/0 0/1
1   15  .   C   A   .   .   DP=3;CALLER=Samtools    GT  .   .   1/1
1   16  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/0 0/0 0/0
1   17  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/1 1/1 1/1

Answer 2

[Pierre Lindenbaum]

(changed)

use picard GatherVcfs : https://broadinstitute.github.io/picard/command-line-overview.html

Answer 3

[cpad0112]

Since both th vcfs belong to same sample and contain identical headers:

$ cat test1.vcf <(awk '!/#/ {print}' test2.vcf)

##fileformat=VCFv4.1 
##FILTER=<ID=PASS,Description="Passed all filters">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Read Depth">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  S1  S2  S3
1   10  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/1 0/0 0/1
1   11  .   C   A   .   .   DP=3;CALLER=Samtools    GT  .   .   1/1
1   12  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/0 0/0 0/0
1   13  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/1 1/1 1/1
1   14  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/1 0/0 0/1
1   15  .   C   A   .   .   DP=3;CALLER=Samtools    GT  .   .   1/1
1   16  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/0 0/0 0/0
1   17  .   C   A   .   .   DP=3;CALLER=Samtools    GT  0/1 1/1 1/1

[Ram]

cough sorting cough

[cpad0112]

Records are already coordinate sorted.

[Ram]

That's not all the data, surely. Better safe than sorry.

Answer 4

[Renesh]

Check this link to merge vcf files https://reneshbedre.github.io/blog/mergevcf.html