Identification and annotation of SNPs and/or somatic mutations compared to reference genome. 10 hour minimum ($470 internal$730 internal, $600 $930 external) per project.
1. Quality Assessment
Quality of data assessed by FastQC and SAMStat; results of quality assessment will be evaluated prior to downstream analysis.
- Deliverables:
- reports generated by FastQC and SAMStat
- metrics specific to hybrid selection analysis calculated using Picard available as well
- Tools Used:
- FastQC: (Andrews 2010) used to generate quality summaries of data:
- Per base sequence quality report: useful for deciding if trimming necessary.
- Sequence duplication levels: evaluation of library complexity.
- Overrepresented sequences: evaluation of adapter contamination.
- SAMStat: (Lassman et. al. 2011) provides summary statistics at both fastq and SAM/BAM alignment levels.
- Picard CalculateHsMetrics: (http://broadinstitute.github.io/picard) evaluates hybrid selection protocols (target coverage and AT/GC dropout levels).
- FastQC: (Andrews 2010) used to generate quality summaries of data:
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