Galaxy |

bcftools view (version 0.1.19.0)

Choose a bcf file to view:

Choose the output format:

-b

List of chromosome names for conversion:

(-D)

Use alternate INDEL-to-SNP mutation rate:

defaults to 0.15 (-i)

Mutation rate for variant calling:

default to 0.001 (-t)

Retain all possible alternate alleles at variant sites:

-A

Output Potential Variant Sites Only:

-v

SNP calling:

Forces -e the max-likelihood inference parameter. (-c)

Suppress all individual genotype information:

-G

Skip sites where the REF field is not A/C/G/T:

-N

Perform max-likelihood inference only:

Including estimating the site allele frequency, testing Hardy-Weinberg equilibrium and testing associations with LRT. (-e)

Call per-sample genotypes at variant sites:

-g

BCFTools View

VCF/BCF conversion, view, subset and filter VCF/BCF files.

Input format

BCF files

Outputs

VCF or BCF files