GenomeComb

Multicompar_reannot

Format

cg multicompar_reannot ?options? compar_file ?force? ?regonly? ?skipincomplete?

Summary

Reannotate multicompar file

Description

cg multicompar-reannot will try to add missing information in a multicompar file (see cg multicompar), such as whether a variant is reference or missing (unsequenced) in a sample that did not contain the variant. To do this, it needs extra information beyond the variant file. It will try to find this information in several locations. It will look for files with this information in sample directories that are siblings to or one dir below the multicompar file. The file sreg-<source>.tsv should minimally be available for reannotation (sequenced or not); if not, an error is given.

Some region files can be used to fix missing information

Coverage (and other) information can be obtained from several sources (if found)

Arguments

compar_file
multicompar file

Options

-force 0/1
if 1, all data will be updated, otherwise only unfilled (indicated with a ?) cells will be updated
-regonly 0/1
if the regonly option is used, only region data (sequenced) will be updated
-skipincomplete 0/1
go on even if data for some samples is not complete (skipping samples which are e.g. missing coverage data for some of the chromosomes)
-paged pagesize
reannot needs to keep a lot of files open, too many for multicompar files with a lot of samples. Using this option reannotation is done per group of pagesize samples. New files have to be written for each group
-pagedstart start
Start paging from a given number (starts with 0). This is useful if a -paged run was interupted, you can restart from where it stopped.

Some options can also be given as words after the argument

force
if present, all data will be updated, otherwise only unfilled (indicated with a ?) cells will be updated
regonly
if the regonly option is used, only region data (sequenced) will be updated
skipincomplete
go on even if data for some samples is not complete (skipping samples which are e.g. missing coverage data for some of the chromosomes)

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