{% extends "template.html" %} {% block table_of_contents %}
  • Read QA/QC
  • Read Mapping
  • Haplotype Calling
  • Genotype Calling
  • {% endblock %} {% block read_len_fig %}

    Figure 1.1: Ridge plot showing the length distribution of input reads.

    {% endblock %} {% block read_len_table %}

    Table 1.1: Uniform read length for each sample.

    {% for i, row in read_length_table.iterrows() %} {% endfor %}
    Sample Length
    {{ row.Sample }} {{ row.Length }}
    {% endblock %} {% block read_filter_stats %}

    Prior to subsequent analysis, reads are filtered for length and ambiguous sequence content. Any read comprised of more than {{"{:.0f}".format(ambiguous_read_threshold * 100)}}% ambiguous bases (N) is discarded. Reads less than {{"{:,}".format(read_length_threshold)}} bp in length are also excluded from all subsequent analysis. (These thresholds can be configured with the --ambiguous-thresh and --length-thresh arguments.)

    Table 1.2: Read filtering metrics.

    {% for sample, stats in qc.items() %} {% endfor%}
    Sample Total Reads Filtered (Ambiguous) Filtered (Length) Reads Kept
    {{sample}} {{stats.total_reads}} {{stats.filtered_ambig}} {{stats.filtered_length}} {{stats.retention}}
    {% endblock %} {% block read_map_header %}

    Filtered reads are aligned to marker reference sequences using BWA MEM and formatted, sorted, and indexed using SAMtools.

    {% endblock %}