RS_Site_Acceptance_Test Protocol

Use this protocol to generate a report displaying site acceptance test metrics.

Filtering Parameters (SFilter v1)

• Minimum Read Length: Reads shorter than this value (in base pairs) are filtered out and excluded from analysis.
• Minimum Subread Length: Subreads shorter than this value (in base pairs) are filtered out and excluded from analysis.
• Minimum Read Quality: Reads with lower quality than this value are filtered out and excluded from analysis.

Mapping Parameters (BLASR v1)

• Maximum Divergence (%): The maximum allowed divergence of a read from the reference sequence.
• Minimum Anchor Size: The minimum size of the read (in base pairs) that must match against the reference sequence.
• Write Output as a BAM File: Specify whether or not to output a BAM representation of the cmp.h5 file.
• Write BED Coverage File: Specify whether or not to output a BED representation of the depth of coverage summary.
• Place Repeats Randomly: Specify that if BLASR maps a read to more than one location with equal probability, then it randomly selects which location it chooses as the best location. If not set, BLASR defaults to the first on the list of matches.

Genomic Consensus v1 (plurality)

Note: Plurality is a very simple variant-calling algorithm which does not perform any local realignment. It is heavily biased by the alignment produced by the mapper, and it is insensitive at detecting indels.

• Output Consensus FASTA and FASTQ Files: Specify whether or not to output FASTA and FASTQ representations of the consensus sequence.
• Write SNPs/Variants as VCF file: Specify whether or not to output a VCF representation of the variants.
• Write SNPs/Variants as BED file: Specify whether or not to output a BED representation of the variants.
• Use Only Unambiguously Mapped Reads: Specify whether or not to filter out reads where Map QV is less than 10. This reduces coverage in repeat regions that are shorter than the read length.