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Old 11-20-2012, 05:52 AM   #1
cardillox
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Location: UK

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Default How to merge two vcf files.

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

Last edited by cardillox; 11-20-2012 at 06:15 AM.
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Old 11-27-2019, 06:47 PM   #2
Evelynarbon
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If you want to combine multiple VCF files into a single one then, you need a third-party tool that easily performs VCF merge in a few clicks. I would like to suggest using the Merge VCF Tool which is easy to use and provide an attractive user-interface to merge VCF.

More Info:- Download Merge VCF Tool
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Old 11-27-2019, 09:19 PM   #3
SNPsaurus
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The merge vcf tool looks to link to a vcard format merger, not the genomic one!
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Old 11-27-2019, 09:25 PM   #4
SNPsaurus
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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/
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