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CLI: import

Synopsis

Convert BCF/VCF/VCF.gz->TWK. Only biallelic diploid genotypes from SNVs will be retained.

Examples

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tomahawk import -i 1kgp3_chr6.bcf -o 1kgp3_chr6
tomahawk import -i 1kgp3_chr6.bcf -b 1000 -L 10 -n 1 -o 1kgp3_chr6

Options

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Options:
  -i FILE  input BCF/VCF/VCF.gz file (required)
  -o FILE  output file prefix (required)
  -f       Flip reference and alternative alleles when major is the alternative allele
  -r       Do NOT filter out variant sites that are univariate for REF or ALT
  -n FLOAT Missingness fraction cutoff (default: 0.95)
  -b INT   Block size (default: 500)
  -L INT   Compression level in range 1-20 (default: 1)
  -s       Hide all program messages [null]