Merge two SNP vcf files

Question

[fufuyou]

File1

#CHROM  POS     ID      REF_Zv  ALT_lm                             
chr1A   219620  .       T       A
chr1A   219648  .       A       G
chr1A   219867  .       A       G

file2

#CHROM  POS     ID      REF_Zv  ALT_RV                             
chr1A   219457  .       C       T
chr1A   219670  .       A       G
chr1A   219867  .       A       C

File3

#CHROM  POS     ID      REF_Zv  ALT_lm ALT_RV                            
chr1A   219620  .       T       A    NA
chr1A   219648  .       A       G    NA
chr1A   219867  .       A       G    C
chr1A   219457  .       C       NA   T
chr1A   219670  .       A       NA   C

My command is

awk 'FNR==NR{a[$1,$2];next} {if(a[$1,$2]==""){a[$1,$2]=0};print $1,$2,$3,$4,$5, a[$4,$5]} ' file1 file2 > file3

However, I can not get the file3 which I want. Could you help me improve the command? Thanks, Fuyou

[Inquisitive8995]

Did you try VCF tools ? They have merge option. http://vcftools.sourceforge.net/perl_module.html

[fufuyou]

But my data has no SNP format. So vcf-merge does not work.

[GenoMax]

@Kevin has examples of the right tool to do this with in: Merging vcf files (intersection and union)

[fufuyou]

My SNP vcf files do not have other columns. such as "GT". Thanks, Fuyou

[WouterDeCoster]

Then those are not vcf files and you make things harder by not using standardised file formats.

Answer 1

[zx8754]

Using R merge:

# example files
file1 <- read.table(text = "#CHROM  POS     ID      REF_Zv  ALT_lm                             
chr1A   219620  .       T       A
chr1A   219648  .       A       G
chr1A   219867  .       A       G", header = TRUE, stringsAsFactors = FALSE,
                    comment.char = "")
file2 <- read.table(text = "#CHROM  POS     ID      REF_Zv  ALT_RV                             
chr1A   219457  .       C       T
chr1A   219670  .       A       G
chr1A   219867  .       A       C", header = TRUE, stringsAsFactors = FALSE,
                        comment.char = "")

merge(file1, file2, by.x = c("X.CHROM", "POS", "ID", "REF_Zv"), all = TRUE)
#   X.CHROM    POS ID REF_Zv ALT_lm ALT_RV
# 1   chr1A 219457  .      C   <NA>      T
# 2   chr1A 219620  .      T      A   <NA>
# 3   chr1A 219648  .      A      G   <NA>
# 4   chr1A 219670  .      A   <NA>      G
# 5   chr1A 219867  .      A      G      C