Question

Combine all chromosomes in a single file

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6.7 years ago

bha ▴ 80

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 • 5.8k views

ADD COMMENT • link updated 6.7 years ago by Bastien Hervé 5.9k • written 6.7 years ago by bha ▴ 80

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bcftools merge may be better. Documentation here.

ADD REPLY • link 6.7 years ago by GenoMax 147k

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Is vcf-tools out of date ?

ADD REPLY • link 6.7 years ago by Bastien Hervé 5.9k

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bcftool concat will be more appropriate?

ADD REPLY • link 6.7 years ago by bha ▴ 80

score 0 · Answer 1 · 2018-04-06

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6.7 years ago

Bastien Hervé 5.9k

To merge vcf you can use vcf-tools merge

ADD COMMENT • link 6.7 years ago by Bastien Hervé 5.9k