How to merge two vcf files.

cardillox · 11-20-2012, 05:52 AM

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 · 11-27-2019, 09:19 PM

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

SNPsaurus · 11-27-2019, 09:25 PM

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 · 01-08-2022, 09:02 AM

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 · 01-09-2022, 04:40 AM

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

Genom · 01-09-2022, 01:49 PM

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

GenoMax · 01-11-2022, 10:21 AM

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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11-20-2012, 05:52 AM	#1
cardillox Junior Member Location: UK Join Date: Nov 2012 Posts: 2	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.

11-27-2019, 09:19 PM	#2
SNPsaurus Registered Vendor Location: Eugene, OR Join Date: May 2013 Posts: 523	The merge vcf tool looks to link to a vcard format merger, not the genomic one! __________________ Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

11-27-2019, 09:25 PM	#3
SNPsaurus Registered Vendor Location: Eugene, OR Join Date: May 2013 Posts: 523	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/ __________________ Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

01-08-2022, 09:02 AM	#4
Genom Junior Member Location: Spain Join Date: Jan 2022 Posts: 6	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

01-09-2022, 04:40 AM	#5
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,143	@Genom: Your question has been answered in https://www.biostars.org/p/9504545/#9504848

01-09-2022, 01:49 PM	#6
Genom Junior Member Location: Spain Join Date: Jan 2022 Posts: 6	It is not possible that the current version is 1.14, because I have 1.3 installed

01-11-2022, 10:21 AM	#7
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,143	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/