Question: Combine all chromosomes in a single file
0
gravatar for bha
2.2 years ago by
bha60
bha60 wrote:

I got 1000 genomes data which is in vcf format. All chromosomes (1 to 22) are in separate files. Is there any way to combine all 22 chromosomes in a single file? My final task is to prune that single file based on MAF and LD. I tried in PLINK (first convert everything in PLINK and tried to merge, but ends up with multi-position variants error, because there are some multiallelics ) . is anyone come across this issue? Any advice please?

genetics • 2.1k views
ADD COMMENTlink modified 2.2 years ago by Bastien Hervé4.6k • written 2.2 years ago by bha60

bcftools merge may be better. Documentation here.

ADD REPLYlink written 2.2 years ago by genomax84k

Is vcf-tools out of date ?

ADD REPLYlink written 2.2 years ago by Bastien Hervé4.6k

bcftool concat will be more appropriate?

ADD REPLYlink written 2.2 years ago by bha60
0
gravatar for Bastien Hervé
2.2 years ago by
Bastien Hervé4.6k
Limoges, CBRS, France
Bastien Hervé4.6k wrote:

To merge vcf you can use vcf-tools merge

ADD COMMENTlink written 2.2 years ago by Bastien Hervé4.6k
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