Table 8 Parameters in LifeScope’s secondary and tertiary analysis software modules
From: Challenges in exome analysis by LifeScope and its alternative computational pipelines
Default value | |
|---|---|
Alignment parameters | |
Minimum number of non-matches allowed during indel finding | 9 |
Maximum deletion size (in a gapped alignment in the first pass) | 19 |
Maximum insertion size (in a gapped alignment in the first pass) | 4 |
The minimum edge length required for insertions and deletions on the first pass | 12 |
Number of mismatches allowed for gap alignments | 3 |
Minimum mapping quality value (MAPQ) allowed for aligned read | 8 |
Minimum edge length required for insertions and deletions | 12 |
The seed window side allowed to the left of the anchor alignment | 40 |
The seed window side allowed to the right of the anchor alignment | 80 |
Maximum number of alignments for a read on the first pass which gives the maximum number of hits that are reported in the mapping output | 50 |
SNPs analysis module using diBayes algorithm variant calling parameters | |
Minimum allele ratio (Het) | 0.15 |
Minimum coverage (Het) | 2 |
Minimum non-reference base QV (Het) | 28 |
Minimum average non-reference base QV (Hom) | 28 |
Minimum base quality value for a position | 28 |
Minimum base quality value of the non-reference allele of a position | 28 |
Mapping quality value of the read | \(>\)8 |
SNP call stringency. Alleles on both strands | Not required |
Threshold of mismatch/alignment-lengh ratio | 1 |
Base candidate allele quality value | \(>\)7 |
Minimum number of unique start positions required to call heterozygote, homozygote | 2 |
Proportion of the total reads containing either of the two candidate alleles | 0.65 |