Description

Call variants from a BAM file using iVar

Input

Name
Description
Pattern

0 ()

1 ()

fasta (file)

The reference sequence used for mapping and generating the BAM file

*.fa

fai (file)

The index for the reference sequence used for mapping and generating the BAM file

*.fai

gff (file)

A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done.

*.gff

save_mpileup (boolean)

Save mpileup file generated by ivar variants

*.mpileup

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

Tools

ivar Documentation

iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing.

License: GPL-3.0-or-later
Authors