GATK4 -Generate sequencing artifact metrics for filtering by orientation bias

Description

Generate sequencing artifact metrics for filtering by orientation bias with GATK4

Parameters

• Reference sequence () [human]
• Chromosome names in my BAM file look like (1, chr1) [chr1]

Details

Collect metrics to quantify single-base sequencing artifacts.

Quantify substitution errors caused by mismatched base pairings during various stages of sample / library prep. We measure two distinct error types - artifacts that are introduced before the addition of the read1/read2 adapters ("pre adapter") and those that are introduced after target selection ("bait bias"). For each of these, we provide summary metrics as well as detail metrics broken down by reference context (the ref bases surrounding the substitution event). For a deeper explanation, see Costello et al. 2013: http://www.ncbi.nlm.nih.gov/pubmed/23303777

Based on GATK4 CollectSequencingArtifactMetrics (Picard) tool. For more detailed information, see GATK documentation,

Output

• <prefix>.bait_bias_summary_metrics.txt
• <prefix>.pre_adapter_detail_metrics.txt
• <prefix>.bait_bias_detail_metrics.txt
• <prefix>.error_summary_metrics.txt
• <prefix>.pre_adapter_summary_metrics.txtArtifact metrics file
• gatk_log.txt

References

This tool is based on the GATK4 package.

For instructions on citing GATK4, please see GATK FAQ