Long indel assembly advanced settings
These parameters control the behavior of the long indel assembler (which is a module within the variantCaller plugin). Again, these parameters are recommended for advanced users only.
Both the FreeBayes module and the long indel assembler generate lists of variant candidates (other modules in the variantCaller plugin then evaluate the candidates). The assembly module attempts to call any indel longer than 3 bp, but only reports indels that fail to be called by the FreeBase module.
|
Parameter |
Description |
|---|---|
|
kmer_len |
Size of the smallest k-mer used in assembly Allowed values: Integers >= 5 Suggested trial value between 11 and 30 Impact: Increasing values make indel calls less sensitive but more specific |
|
min_var_freq |
Minimum frequency of the variant to be reported Allowed values: Decimal numbers between 0 and 1 Suggested trial value between 0.1 and 0.4 Impact: Increasing values make indel calls less sensitive but more specific |
|
min_var_count |
Minimum support for a variant to be evaluated Allowed values: Integers > 1 Suggested trial value between 3 and 30 Impact: Increasing values make indel calls less sensitive but more specific |
|
short_suffix_match |
Minimum assembled sequence match on both sides of the variant Allowed values: Integers > 2 Suggested trial value between 4 and kmer_len Impact: Increasing values make indel calls less sensitive but more specific |
|
min_indel_size |
Minimum size indel reported by assembly Allowed values: Integers > 0 Suggested trial value between 2 and 30 Impact: Increasing values make indel calls less sensitive but more specific |
|
max_hp_length |
Variants containing HP larger than this are not reported Allowed values: Integers > 1 Suggested trial value between 2 and 11 Impact: Increasing values make indel calls more sensitive but less specific |
|
relative_strand_bias |
Variants with strand bias above this are not reported Allowed values: Decimal numbers between 0 and 1 Suggested trial value between 0.6 and 1.0 Impact: Increasing values make indel calls more sensitive but less specific |
|
output_mnv |
Enables reporting of complex variants Allowed values: 1 = report complex variants, 0 = don't report Suggested trial value 0 |