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informationsea/sequencetoolkit

By informationsea

•Updated about 2 years ago

Toolkit for Genome Sequence Analysis

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informationsea/sequencetoolkit repository overview

⁠sequencetoolkit

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Toolkit for Genome Sequence Analysis

⁠Features

⁠BED Utilities
  1. Merge overlapped regions
  2. Expand region size
⁠Gene Annotation Utilities
  1. Convert CDS/Transcript position into genomic position
  2. Convert genomic position into CDS/Transcript position
⁠VCF Utilities
  1. Add GenotypeCount and nhomalt INFO tags.
  2. Convert a VCF file to CSV, TSV and Excel file.
  3. Replace contig names.
  4. Replace sample names.
  5. Remove INFO tags.
  6. Remove FORMAT tags.
  7. Remove non-standard headers.
  8. Generate CREATE TABLE SQL from VCF file.

⁠Usage

⁠Add Genotype Count

Add or rewrite allele frequency, count, number and genotype count

USAGE:
    sequencetoolkit vcfutils add-af [OPTIONS] [--] [input]

FLAGS:
    -h, --help       Prints help information
    -V, --version    Prints version information

OPTIONS:
    -c, --category <category>    category mapping file (csv or tsv)
    -i, --id <id>...             ID column name in category mapping file
    -o, --output <output>        Output CSV
    -v, --value <value>...       value column name in category mapping file

ARGS:
    <input>    Input VCF file

First line in a category mapping file is used as header. If you use category mapping file, id and value options are required.

⁠Example
  • category.csv
id,sex,protocol
SAMPLE1,M,HiSeq2500
SAMPLE2,F,HiSeq2500
SAMPLE3,M,NovaSeq600
SAMPLE4,F,NovaSeq600

vcfutils add-af --output output.vcf.gz --category category.csv --id id --value sex protocol -- input.vcf.gz

Note: output vcf file is not compressed with bgzip.

⁠Convert a VCF file to CSV, TSV or Excel file
USAGE:
    sequencetoolkit vcfutils vcf2csv [FLAGS] [OPTIONS] [--] [input]

FLAGS:
    -d, --decode-genotype        Decode GT format tag number into alleles
    -h, --help                   Prints help information
    -m, --split-multi-allelic    Split multi allelic sites into multiple lines
    -V, --version                Prints version information

OPTIONS:
    -c, --canonical-list <canonical-list>    Canonical transcript list (created with extract-canonical command)
    -t, --data-type <datatype>               Data type to output [default: auto]  [possible values: auto,
                                             xlsx, csv, tsv]
    -f, --format <format>...                 FORMAT tags to include
    -i, --info <info>...                     INFO tags to include
    -o, --output <output>                    Output file

ARGS:
    <input>    Input VCF file
⁠Replace contig names
USAGE:
    sequencetoolkit vcfutils replace-contig [FLAGS] [OPTIONS] --contig-mapping <contig-mapping> [input]

FLAGS:
    -a, --add-chr-prefix       add "chr" prefix to human chromosomes
    -h, --help                 Prints help information
    -r, --remove-chr-prefix    remove "chr" prefix from human chromosomes
    -e, --replace-refseq       Replace RefSeq contig name with chromosome number (for dbSNP 152/153)
    -V, --version              Prints version information

OPTIONS:
    -m, --contig-mapping <contig-mapping>    contig mapping file (csv/tsv)
    -o, --output <output>                    Output file

ARGS:
    <input>    Input VCF file

Note: contig mapping file should not include header line. A first column should be original contig name, and a second column should be new contig name.

⁠Replace sample names
USAGE:
    sequencetoolkit vcfutils replace-sample-names [FLAGS] [OPTIONS] --sample-mapping <mapping> [input]

FLAGS:
    -h, --help                 Prints help information
    -r, --random               Shuffle sample order
    -s, --rename-sequential    Rename sample as "sample_1", "sample_2", ...
    -V, --version              Prints version information

OPTIONS:
    -m, --sample-mapping <mapping>    sample name mapping file (csv/tsv)
    -o, --output <output>             Output VCF file

ARGS:
    <input>    Input VCF file
⁠Rewrite format

Remove unnecessary FORMAT tags.

USAGE:
    sequencetoolkit vcfutils rewrite-format [OPTIONS] [--] [input]

FLAGS:
    -h, --help       Prints help information
    -V, --version    Prints version information

OPTIONS:
    -e, --exclude-info-list <exclude>...    Black list of format tags
    -f, --format-list <format>...           White list of format tags
    -o, --output <output>                   Output file

ARGS:
    <input>    Input VCF file
⁠Rewrite INFO

Remove unnecessary INFO tags.

USAGE:
    sequencetoolkit vcfutils rewrite-info [OPTIONS] [--] [input]

FLAGS:
    -h, --help       Prints help information
    -V, --version    Prints version information

OPTIONS:
    -e, --exclude-info-list <exclude>...    Black list of format tags
    -i, --info-list <info>...               White list of info tags
    -o, --output <output>                   Output file

ARGS:
    <input>    Input VCF file
⁠Expand BED regions
USAGE:
    sequencetoolkit bedutils expand [OPTIONS] --expand <expand> [input]

FLAGS:
    -h, --help       Prints help information
    -V, --version    Prints version information

OPTIONS:
    -e, --expand <expand>                Expand length
    -n, --expand-end <expand-end>        Expand length
    -s, --expand-start <expand-start>    Expand length
    -o, --output <output>                Output Text

ARGS:
    <input>...    Input BED files
⁠Merge overlapped regions
USAGE:
    sequencetoolkit bedutils merge [OPTIONS] [input]...

FLAGS:
    -h, --help       Prints help information
    -V, --version    Prints version information

OPTIONS:
    -o, --output <output>    Output Text

ARGS:
    <input>...    Input BED files

Tag summary

Content type

Image

Digest

Size

19.3 MB

Last updated

about 5 years ago

docker pull informationsea/sequencetoolkit