Expand¶
The expand command explodes a VCF file into a tab-separated file. It is not caller-dependent and will work with any VCF file.
Usage¶
$ jacquard expand <input_file> <output_file> [OPTIONS]
positional arguments:
input_file | A VCF file
|
output_file | A tab separated text file
|
optional arguments:
-s, –selected_columns_file FILE | File containing an ordered list of
column names to be included
in the output file; column names can
include regular expressions
|
Description¶
Expand command converts a VCF file into a tab-delimited file. This format is more suitable than a VCF for analysis and visualization in R, Pandas, Excel, or another third-party application.
Note¶
- The ‘fixed’ fields (i.e. CHROM, POS, ID, REF, ALT, QUAL, FILTER) are directly copied from the input VCF file.
- Based on the metaheaders, each field in the INFO column is expanded into a separate column named after its tag ID.
- Each FORMAT tag is expanded into a set of columns, one for each sample, named as <FORMAT tag ID>|<sample column name>.
- By default, all INFO fields and FORMAT tags are expanded; specific INFO fields and FORMAT tags can be selected using the –selected_columns_file option.
- Expand also emits a tab-delimited glossary file, based on the metaheaders in the input VCF file. FORMAT and INFO tag IDs are listed in the glossary and are defined by their metaheader description.