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Call variants (version 2.1.5+galaxy2)
Note: To have indels included in the called variants you HAVE to preprocess your input data using lofreq indelqual to include indel qualities. In addition, it is highly recommended that you calculate and make use of indel alignment qualities. See the detailed tool help below.

lofreq call: call variants from BAM file

LoFreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing, which are usually ignored by other methods or only used for filtering.

LoFreq can run on almost any type of aligned sequencing data since no machine- or sequencing-technology dependent thresholds are used. It automatically adapts to changes in coverage and sequencing quality and can therefore be applied to a variety of data-sets e.g. viral/quasispecies, bacterial, metagenomics or somatic data.

While the tool will often give reasonable results with default settings a variety of options let you control its exact behavior. These advanced options can be subdivided into those affecting variant calling and those affecting posterior filtering of the results.

Variant calling paramters

At the heart of LoFreq's variant caller is a joint quality score that is computed for every site in every read (that survives filtering) and that combines some or all of the following read and base quality measures:

Variant filter parameters

After generating a list of called variants, the tool can filter this list based on:

While posterior filtering can help reduce false-positive variant calls, please note that the separate lofreq filter, which can be run on the output of lofreq call has many more options for configuring filters.

These are the different filter settings supported by the tool:

Preset filtering on QUAL score + coverage + strand bias

For variants to pass this filter, the following is required:

Preset QUAL score-based filtering

Same QUAL-based significance filter as the default, but without the strand-bias and coverage criteria

Strictly no filtering

Do not apply any filters, but produce the original list of all called variants. You will almost always want to use lofreq filter to process the resulting output.

Custom filter settings/combinations

Lets you define your own QUAL-based significance filter and, optionally, combine it with the default starnd-bias and coverage filters.