Table 9 List of open source tools used in our study of the alternatives to the LifeScope pipeline
From: Challenges in exome analysis by LifeScope and its alternative computational pipelines
Analysis category | Tool | Web reference |
|---|---|---|
Convert XSQ to color-space fastq | XSQtools solid2fastq | Life Technologies website Bfast package |
Alignment to the reference genome | Maq v.0.7.1 | |
Default parameters, -n 3 | ||
Shrimp 2.2.3 | ||
Default parameters, -h 85 –strata -o 3 | ||
Bfast 0.7.0 | ||
Default parameters | ||
Preprocessing | Picard 1.111 | |
Samtools 0.1.18 | ||
Variant calling | GATK v.3.1 | |
Steps and parameters in Table 7 | ||
Variant summaries | Vcftools 0.1.12 | |
Bcftools v.0.2.0 | ||
Variant annotation | Annovar | |