Bcftools consensus sample
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5 months ago
Dragod ▴ 10

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

sample Bcftools consensus • 495 views
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it's clearly defined in the manual : http://samtools.github.io/bcftools/bcftools.html#consensus

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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?

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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",

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

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Is it a file or just a sample name?

why don't you just try ?

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