freyja variants

Perform variant calling using samtools and iVar on a BAMFILE

freyja variants [OPTIONS] BAMFILE

Options

--ref <ref>

Reference file in fasta format

Default:

data/NC_045512_Hu-1.fasta

--variants <variants>

Variant calling output file

--depths <depths>

Sequencing depth output file

--refname <refname>

Ref name (for bams with multiple sequences)

--minq <minq>

Minimum base quality score

--annot <annot>

provide an annotation file in gff3 format

--varthresh <varthresh>

Variant frequency threshold

Default:

0.0

Arguments

BAMFILE

Required argument

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Example Usage:

After primer trimming in iVar, we get both variant call and sequencing depth information with the command: freyja variants [bamfile] --variants [variant outfile name] --depths [depths outfile name] --ref [reference.fa] which uses both samtools and iVar. Note that the reference should match the fasta file used for alignment. In cases where multiple reference genomes are present in the reference fasta, the user can specify the name of the desired reference genome with --refname [name-of-reference]. To enable alternative variant calling methods ( such as LoFreq), we also allow users to provide a VCF file using the --variants option (in addition to the usual depth file, which can be obtained using a command like samtools mpileup -aa -A -d 600000 -Q 20 -q 0 -B -f ref.fasta sample.bam | cut -f1-4 > sample.depth).