Bcftools consensus sample

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3.5 years ago

Dragod ▴ 10

What I need to input for the -s option in bcftools consensus?

sample Bcftools consensus • 1.8k views

ADD COMMENT • link updated 3.5 years ago by Pierre Lindenbaum 164k • written 3.5 years ago by Dragod ▴ 10

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it's clearly defined in the manual : http://samtools.github.io/bcftools/bcftools.html#consensus

ADD REPLY • link 3.5 years ago by Pierre Lindenbaum 164k

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So what is the meaning of "Using the --sample (and, optionally, --haplotype) option will apply genotype (haplotype) calls from FORMAT/GT"? What is the meaning of NA001 in the provided example? "bcftools consensus -i -s NA001 -f in.fa in.vcf.gz > out.fa " just a name or any file with specific format needed?

ADD REPLY • link 3.5 years ago by Dragod ▴ 10

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? What is the meaning of NA001 in the provided example?

http://samtools.github.io/bcftools/bcftools.html#consensus

Apply variants present in sample "NA001",

ADD REPLY • link 3.5 years ago by Pierre Lindenbaum 164k

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Is it a file or just a sample name? How to record these variants for this sample?

ADD REPLY • link 3.5 years ago by Dragod ▴ 10

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Is it a file or just a sample name?

why don't you just try ?

ADD REPLY • link 3.5 years ago by Pierre Lindenbaum 164k

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