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What is Bgzip?
DESCRIPTION. Bgzip compresses files in a similar manner to, and compatible with, gzip(1). The file is compressed into a series of small (less than 64K) ‘BGZF’ blocks. This allows indexes to be built against the compressed file and used to retrieve portions of the data without having to decompress the entire file.
What does BCFtools view do?
DESCRIPTION. BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
Is Bgzip part of Samtools?
samtools / tabix Public archive Note: tabix and bgzip binaries are now part of the HTSlib project.
What is Tabix?
Tabix is the first generic tool that indexes position sorted files in TAB-delimited formats such as GFF, BED, PSL, SAM and SQL export, and quickly retrieves features overlapping specified regions.
How do I view a VCF GZ file?
To view the file you can use simply zmore command, VCF is just a text table and compressed with Gzip/Bgzip, also tabix can help you to extract some positions.
Is Tabix part of Samtools?
GitHub – samtools/tabix: Note: tabix and bgzip binaries are now part of the HTSlib project.
What is a TBI file?
What is a TBI file? A . TBI file is an Image for Windows Disk Image file. Through our analysis of TBI files, we know that one use of the format is Image for Windows Disk Image.
What happens when a file is compressed in bgzip?
If a file is specified, it will be compressed (or decompressed with -d). If the -c option is used, the result will be written to standard output, otherwise when compressing bgzip will write to a new file with a .gz suffix and remove the original.
What kind of files can I use with bcftools?
Some helper scripts are bundled with the bcftools code. Files can be both VCF or BCF, uncompressed or BGZF-compressed. The file “-” is interpreted as standard input. Some tools may require tabix- or CSI-indexed files.
Can a bgzipped BCF stream work with VCF?
Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
How are the regions specified in bcftools GitHub page?
Regions can be specified either on command line or in a VCF, BED, or tab-delimited file (the default). The columns of the tab-delimited file can contain either positions (two-column format) or intervals (three-column format): CHROM, POS, and, optionally, END, where positions are 1-based and inclusive.