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

    Figure 1.1: Ridge plots showing the length distribution of input R1 (left) and R2 (right) reads.

    {% endblock %} {% block read_len_table %}

    Table 1.1: Uniform read lengths for each sample.

    {% for i, row in read_length_table.iterrows() %} {% endfor %}
    Sample Length R1 Length R2
    {{ row.Sample }} {{ row.LengthR1 }} {{ row.LengthR2 }}
    {% endblock %} {% block read_filter_stats %}

    Prior to subsequent analysis, reads are filtered for ambiguous sequence content. Any read comprised of more than {{"{:.0f}".format(ambiguous_read_threshold * 100)}}% ambiguous bases (N) is discarded, along with its mate. (This threshold can be configured with the --ambiguous-thresh argument.) The table below shows the number of read pairs that were removed from each sample and which read(s) in the pair exceeded the filtering threshold.

    Table 1.2: Metrics for read filtering based on ambiguous content.

    {% for sample, stats in qc.items() %} {% endfor %}
    Sample Total Pairs R1 Only Failed R2 Only Failed Pair Failed Pairs Removed Pairs Kept Retention
    {{sample}} {{stats.ambig.total_reads}} {{stats.ambig.excluded_r1}} {{stats.ambig.excluded_r2}} {{stats.ambig.excluded_both}} {{stats.ambig.excluded}} {{stats.ambig.retained}} {{stats.ambig.retention_rate}}
    {% endblock %} {% block read_merge_stats %}

    Read Merging

    Paired end reads are merged using FLASh. Merged reads less than {{"{:,}".format(read_length_threshold)}} bp in length are filtered out prior to read mapping and excluded from all subsequent analysis. (This threshold can be configured with the --length-thresh argument.)

    Table 2.1: Read merging metrics.

    {% for sample, stats in qc.items() %} {% endfor %}
    Sample Filtered Reads Merged Reads Merge Rate
    {{sample}} {{stats.merge.total_reads}} {{stats.merge.merged_reads}} {{stats.merge.merge_rate}}

    Figure 2.2: Ridge plot showing the length distribution of merged reads.

    Table 2.3: Metrics for read length filtering.

    {% for sample, stats in qc.items() %} {% endfor %}
    Sample Total Merged Reads Reads Removed Reads Kept Retention
    {{sample}} {{stats.length.total_reads}} {{stats.length.excluded}} {{stats.length.kept}} {{stats.length.retention_rate}}
    {% endblock %} {% block read_map_header %}

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

    {% endblock %}