Merge vcf files from Multiple Samples

Question

[Ron]

Hi,

I want to merge vcf files of same format from multiple samples using vcf-tools.But I want to know which method among vcf-merge or vcf-concat should I use for viewing results .Sample name does not matter in results.

This is the current format of each vcf file.

#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    SampleName

Thanks

Answer 1

[Devon Ryan]

You would want vcf-merge. Concatenating means linking together like in a chain (so end-to-end).

[Ron]

I used vcf-merge, after sorting,bgzip and using tabix.Everything went well.But while merging I am getting this error below:My sample names are Clk51764 and Clk51769 as I am just testing the merge on 2 samples.

Using column name 'Clk51764' for 51764.sort.vcf.gz:Clk51764
Using column name 'Clk51769' for 51769.sort.vcf.gz:Clk51769
Could not determine the ploidy (nals=2, nvals=10). (TODO: ploidy bigger than 2)
6
 at /vcftools_0.1.12/perl//Vcf.pm line 172
    Vcf::throw('Vcf4_1=HASH(0x28a4e00)', 'Could not determine the ploidy (nals=2, nvals=10). (TODO: plo...', 6) called at /vcftools_0.1.12/perl//Vcf.pm line 2404
    VcfReader::guess_ploidy('Vcf4_1=HASH(0x28a4e00)', 2, 10) called at /vcftools_0.1.12/perl//Vcf.pm line 1760
    VcfReader::parse_AGtags('Vcf4_1=HASH(0x28a4e00)', 'HASH(0x2909ab8)') called at /vcftools_0.1.12/bin/vcf-merge line 464
    main::merge_vcf_files('HASH(0x289cc20)') called at /vcftools_0.1.12/bin/vcf-merge line 12

[Devon Ryan]

What's the ploidy of your organism? VCF-tools apparently still only supports diploids.

[devenvyas]

I am getting a similar error message. Did you ever manage to get vcf-merge to work?

Answer 2

[mtaschuk]

If you can disregard the sample name (i.e. you're only interested in whether the SNPs are present, not where they came from), you can cut the first 9 columns, concatenate them together, and then run uniq over the resulting file.

for i in `ls *vcf`; do cut -f1-9 $i | grep -vE "^#" >> fullfile.vcf; grep ^# $i>uniqfile.vcf; done; sort fullfile.vcf | uniq > uniqfile.vcf

Not tested so syntax might not be exact, but something like that will serve.

Edit: trying to make the code properly formatted

Answer 3

[wasixo5225]

If you want to learn how to merge multiple VCF files, I recommend utilizing the outlook VCF merge tool. With this software, you can merge numerous VCF files into one. This software has more advanced functions, such as the ability to remove duplicate pst file items.

Visit at : https://www.osttopstapp.com/merge-vcf.html