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

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
vcf
• 13,828 views • link
updated by rigolif501 • rigolif501 • written by humeira.tayyab • humeira.tayyab

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. Formatting bar

• 1 views • link
written by Ram Ram

4 answers

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
• 1 views • link
written by Kevin Blighe Kevin Blighe

(changed)

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

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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
• 1 views • link
written by cpad0112 cpad0112

cough sorting cough

• 1 views • link
written by Ram Ram

Records are already coordinate sorted.

• 1 views • link
written by cpad0112 cpad0112

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

• 1 views • link
written by Ram Ram

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

• 0 views • link
written by Renesh Renesh

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