allow_indels

Candidate generation parameter: Allow indel candidates to be generated when set

Allowed values: 1 = generate indel candidates, 0 = don't generate

Suggested trial value 1

allow_snps

Candidate generation parameter: Allow SNP candidates to be generated when set

Allowed values: 1 = generate SNP hypotheses, 0 = don't generate

Suggested trial value 1

allow_mnps

Candidate generation parameter: Allow MNP candidates to be generated when set

Allowed values: 1 = generate MNP hypotheses, 0 = don't generate

Suggested trial value 1

allow_complex

Candidate generation parameter: Allow complex variant candidates to be generated when set

Allowed values: 1 = generate MNP hypotheses, 0 = don't generate

Suggested trial value 1

gen_min_alt_allele_freq

A candidate generation parameter: A non-HP-indel candidate needs to have an allele frequency greater than this value in the pileup

Allowed values: Decimal numbers between 0 and 1

Suggested trial value between 0.02 and 0.15

gen_min_indel_alt_allele_freq

A candidate generation parameter: An HP-indel candidate needs to have an allele frequency greater than this value in the pileup

Allowed values: Decimal numbers between 0 and 1

Suggested trial value between 0.02 and 0.15

gen_min_coverage

A candidate generation parameter: A variant candidate location needs to have coverage depth greater than this value

Allowed values: Integers >= 0

Suggested trial value 6

min_mapping_qv

A candidate generation and variant evaluation parameter: Minimum mapping quality value required for a read to be considered (for both candidate generation and variant evaluation)

Allowed values: Integers >= 0

Suggested trial value 4

read_snp_limit

Do not use reads with number of snps above this

Allowed values: Integers >= 0

Suggested trial value 10

read_max_mismatch_fraction

A candidate generation parameter: Ignore reads with fraction of mismatch greater than this value

Allowed values: Decimal numbers between 0 and 1

Suggested trial value 1.0

tvcargs

This field is for internal use.

Recommended value: "tvc"

tmapargs

The desirable arguments for aligning the BAM file. Recommended value: "tmap mapall . . . -J 25 --end-repair 15 --do -repeat-clip --context stage1 map4" (ampliseq), "tmap" (others)|