Package for loading data from bcf files

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pybcf

This is a package for reading BCF files (binary call format). Similar to pysam/cyvcf2, but limited to reading from BCF files only, and oriented around getting genotype data into numpy arrays quickly.

'''py from pybcf import BcfReader

bcf = BcfReader(bcf_path)

for var in bcf: # the usual attributes are available e.g. # var.chrom, var.pos, var.ref, var.alts, var.info['AF']

# get genotypes as numpy array
genotypes = var.samples['GT']  # as numpy array, missing=-1

'''

Limitations

  • can't fetch variants from random regions yet
  • not extensively tested yet
  • extracting info fields is slow at the moment

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1.3.7

1.3.6

1.3.5

1.3.4

1.3.3

1.3.2

1.3.1

1.3.0

1.2.0

1.1.0

1.0.2

1.0.1

This version

1.0.0

0.99.0

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