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BBTools: call variants (version 39.08+galaxy3)

Bam file:

Bam files produced by BBMap are recommended

Select reference genome source; a cached reference or one from the history:

Using reference genome:

Ploidy:

See help section below

Select output format:

Output variant score histogram?:

Output zygosity histogram?:

Output quality histogram?:

What it does

CallVariants is a high-speed, multithreaded variant caller that accepts bam files, and output VCF files. It is capable of indel realignment, multi-sample variant-calling, and processing samples with arbitrary ploidy.

BBMap is the recommended mapping program for CallVariants, but output from any aligner is acceptable. Reads can be realigned with the "realign" flag. This is slower, but is highly recommended if the input is from any mapping tool other than BBMap. Output from BBMap should not be realigned.

Options

Ploidy - Arbitrary ploidy is supported - the default is 1 which works for haploid organisms. Allele fractions lower than those expected for the ploidy (for example, anything below 0.5 for a diploid, or 0.25 for a tetraploid) will incur a score penalty. When calling variants on non-haploid organisms, it is crucial to set the ploidy.