vcf_format_conversions.py: VCF to Plink/EIGENSTRAT

Automates various simple file conversions. Currently the function is capable of converting between VCF-based formats (i.e. VCF, compressed-VCF, and BCF) and PLINK-based formats (i.e. PED and Binary-PED). Additional formats will be added as needed.

Input Command-line Arguments

--vcf <vcf_filename>

Argument used to define the filename of the VCF file.

--vcf-fid <fid_str>

Argument used to define the family ID for all VCF samples.

--ped-prefix <ped_prefix>

Argument used to define the filename prefix of both PED and MAP files.

--ped <ped_filename>

Argument used to define the filename of the PED file. Called alongside --map.

--map <map_filename>

Argument used to define the filename of the MAP file. Called alongside --ped.

--binary-ped-prefix <binary_ped_prefix>

Argument used to define the filename prefix of the Binary-PED, FAM, and BIM files.

--binary-ped <ped_filename>

Argument used to define the filename of the Binary-PED (i.e. BED) file. Called alongside --fam and --bim.

--fam <fam_filename>

Argument used to define the filename of the FAM file. Called alongside --binary-ped and --bim.

--bim <bim_filename>

Argument used to define the filename of the BIM file. Called alongside --binary-ped and --fam.

Output Command-line Arguments

--out <output_filename>

Argument used to define the complete output filename, overrides --out-prefix.

--out-prefix <output_prefix>

Argument used to define the output prefix (i.e. filename without file extension).

--out-format <vcf, vcf.gz, bcf, ped, ped-12, binary-ped, eigenstrat>

Argument used to define the desired output format. Formats include: uncompressed VCF (vcf); compressed VCF (vcf.gz); BCF (bcf); PLINK text file (ped); PLINK "12" coded text file (ped-12); binary PLINK file (binary-ped); and eigenstrat file (eigenstrat).

--overwrite

Argument used to define if previous output should be overwritten.

Other Command-line Arguments

--delete-original

Argument used to define that the original file should be deleted once converted.

--threads <thread_int>

Argument used to define the number of threads. This argument is currently only supported by conversions to/from PED and Binary-PED.