bcftools error in variant calling chapter

Question

[EHSAN]

Hi,

I am reading through the variant calling chapter of biostar book and faced a problem at below step:

# Compute the genotypes from the alignment file.
bcftools mpileup -Ovu -f $REF $BAM > genotypes.vcf

# Then I get this error:
Could not parse argument: --output-type u

It would be very appreciated if someone can help. Many thanks.

Answer 1

[Istvan Albert]

The valid output types are:

  -O, --output-type TYPE  'b' compressed BCF; 'u' uncompressed BCF;
                          'z' compressed VCF; 'v' uncompressed VCF; 0-9 compression level [v]

this might be a typo in the book the correct line is:

bcftools mpileup -Ov -f $REF $BAM > genotypes.vcf

see also the recipe at:

https://www.bioinformatics.recipes/recipe/view/recipe-bcftools/

[EHSAN]

Thanks Istvan, true, that was a typo.