View source for Vcf2geno

= vcf2geno =

Convert VCF files to genotype file and site file.

== Input File ==

Vcf2geno takes VCF files. They can be in plain text or GZIP/BGZIP compressed formats.

== Outputs ==

Vcf2geno generates two sets of first: prefix.geno and preifx.site where ''prefix'' is the given parameter to ''--out''.

A .geno file is shown below:

<pre>X1  X1  0   -9  0   0   0   2   2   2   2   2   2
X2  X2  -9  -9  0   0   0   2   2   2   2   2   2
X3  X3  0   -9  0   0   0   2   2   2   2   2   2
X4  X4  0   -9  0   0   0   2   2   2   2   2   2
X5  X5  0   -9  0   0   0   2   2   1   2   2   2
X6  X6  0   -9  0   0   0   2   2   2   2   2   -9</pre>
The first and second columns are sample IDs copied from the header of VCF files. From column 3 till the last the column, they are individual level genotype converted from VCF files.

A .site file is shwon below:

<pre>CHROM   POS ID  REF ALT
1   10  1:10    A   T
1   20  1:20    G   C
1   30  1:30    C   A
1   40  1:40    A   C
1   10000   1:10000 G   C
1   20000   1:20000 T   A
4   5000    4:5000  A   T
4   6000    4:6000  C   T
X   800 X:800   A   C
X   900 X:900   A   T
X   1000    X:1000  T   G</pre>
The content of .site file begins with a header line, and thus the content part from the second line is chromosome, positions, reference alleles and alternative alleles.

== Options ==

Vcf2geno provides samplexs selection options and range selection options.

There are four options to include/exclude samples: --peopleIncludeID, --peopleExcludeID: specify which samples are included/excluded in conversion, e.g. --peopleIncludeID X1,X2,X3 will convert only 3 people during conversion if input VCF file contains these three samples. --peopleIncludeFile, --peopleExcludeFile: speicify a file to include/exclude samples. Each line of the file should be a sample ID.

There are two options to specify regions. You can convert part of the VCF file using this option, however, your input file must be indexed by TABIX. --rangeList: this options enable you to speicify a range by hand. e.g. --rangeList 1:100-200. Note your chromosome name in the command line should be consistent to the content of the VCF file (e.g. both do not have 'chr' prefix). --rangeFile: this optinos speicify range by a given file. Each line of the file should specify a range, e.g. '1:100-200' or alternatively three columns '1 100 200'.

== Example ==

Under the &quot;exampleVCF&quot; folder, you can file example.vcf.gz. This is an indexed VCF file. Basica usage of extracting all samples across all regions:

<pre>../vcf2geno --inVcf example.vcf.gz --out test</pre>
Convert sample X1 from range 1:20-30: ../vcf2geno --inVcf example.vcf.gz --rangeList 1:20-30 --peopleIncludeID X1 --out test