How to merge two vcf files.

[cardillox]

Dear all,
I am really a newbie in NGS analysis, so I am really sorry if I am wrong.

I have 4 vcf files and I would like to merge them.

The problem is that 3 of them contain not only the variants but every position from ~60k to ~130M bp (http://cdna.eva.mpg.de/denisova/VCF/human/) and 1 files in bam format. What I have done is to call the variants with mpileup and created the vcf files from the unique bam file that i had.
Which is in your opinioon the best way to merge all this 4 files? vcf-merge in vcftools could be an option but create a huge files, what i would like to have is a vcf file with the mutations for my 4 samples.

In addition I would like to add ID information fpr each SNP, is it vcf annotate a good option?

Thank you very much in advanc for four help.

Have a nice day

Francesco

[SNPsaurus]

The merge vcf tool looks to link to a vcard format merger, not the genomic one!

[SNPsaurus]

Francesco, I didn't quite understand what you have, but if you have a large merged vcf and want to reduce it to a specific region of the genome or only show polymorphic SNPs in your 4 samples then you can filter the large vcf into something more manageable with vcftools http://vcftools.sourceforge.net/

[Genom]

files bam for itv

How could I join eight bam files, which I used to have in sam, and before is fastq
I have used samtools merge command, but it does not give result
is to see it in igv,
tell me different ideas

[GenoMax]

@Genom: Your question has been answered in https://www.biostars.org/p/9504545/#9504848

[Genom]

It is not possible that the current version is 1.14, because I have 1.3 installed

[GenoMax]

That numbering is odd. Versions went from 1.3, 1.4 to 1.10,1.11,1.12 etc. Currently 1.14.

See: https://github.com/samtools/samtools/releases/

[jerebajsmith]

If you are searching to merge two VCF files into one and you do not know about the process of how to combine multiple VCF files into one file. I will suggest an article about Merge Two VCF files. This article provides all essential information and explained the various methods of Merge or Combine VCF files into one file.

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