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CHANGELOG.md

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Change log Version 1.0.1

Usage:

gVCF2tFasta -v input.vcf(.gz) -r reference.fa(.gz) -c ploidy [-o outputname] [-n chromosomes.txt] [-i 0/1]
  • add -c INT option to take ploidy as input

Change log Version 1.0.0

Usage:

gVCF2tFasta -v input.vcf(.gz) -r reference.fa(.gz) [-o outputname] [-n chromosomes.txt]

Note: Structural Variants are considered as missing data (N)

gVCF2tFasta arguments/options:

    -h              Help and exit
    -v              Input VCF file
    -r              Reference Fasta file
    -o              Optional Output compressed tFasta filename, Default same as input vcf file
    -n              Optional File with chromosome(s) to convert and its length, Default use all sequences as in reference fasta file
    -i              Imputation (Only use with VCF files, not gVCF files):
                    0 if missing data in VCF is equal to N in tFasta
                    1 if missing data in VCF is equal to reference fasta in tFasta
                    Default value is 0

Input and Output Files

Input Files and Flags

  • VCF file (input.vcf(.gz)) : accepts both uncompressed and compressed files (gzip , bgzip). The input VCF file must be sorted.
  • Reference Fasta file (reference.fa(.gz)) : accepts both uncompressed and compressed files (only bgzip). An index file (.fai) is created for the reference fasta file if it does not exist.
  • File with chromosome(s) to convert and its length (chromosomes.txt) : Optional File with chromosome(s) to convert and its length, Default use all sequences as in reference fasta file, if not provided.
  • Output compressed tFasta filename (outputname) : Optional Output compressed tFasta filename, Default same as input vcf file, if not provided.
  • Imputation (Only use with VCF files, not gVCF files) : 0 if missing data in VCF is equal to N in tFasta, 1 if missing data in VCF is equal to reference fasta in tFasta, Default value is 0.

Output Files

  • Output tfasta file : The output tfasta file is compressed (bgzip).
  • Index file : An index file (.tbi) is created for the output tfasta file.