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= 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 "exampleVCF" 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
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 "exampleVCF" 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
