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Old 11-20-2012, 05:52 AM   #1
cardillox
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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, 09:19 PM   #2
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   #3
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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Old 01-08-2022, 09:02 AM   #4
Genom
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Default 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
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Old 01-09-2022, 04:40 AM   #5
GenoMax
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@Genom: Your question has been answered in https://www.biostars.org/p/9504545/#9504848
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Old 01-09-2022, 01:49 PM   #6
Genom
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It is not possible that the current version is 1.14, because I have 1.3 installed
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Old 01-11-2022, 10:21 AM   #7
GenoMax
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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/
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