sage v3.4

Functional

• sync overlapping fragments on by default
• sync overlapping fragments logic: favor longer INDELs for CIGAR mismatch, forms consensus no matter how many bases are mismatching, ignore 3’ side of overlap where insert size < read length
• VCF writes AMQ (average map qual), ANM (average events per read) and MED (max edged distance)
• soft-filter average map qual for ref vs alt reads if different > 15
• average base qual filter lowered from 28 to 25
• new modMAPQ logic supports calling low mapq regions (default behaviour unchanged)
• added read strand bias filter
• added maxEdgeDistance filter
• AF filter can pass with lower AF if p-value condition met
• new deduplication logic for INDELs logic handles 1:M deduplication

Targeted panel mode, enabled with config 'high_depth_mode':

• ignore all reads with AD<30
• ignore all soft clip support
• added jitter AF filter
• BQR ignores overlapping bases

Bugs

• fragment strand bias calculated incorrectly

HTML Visualisations added for variants:

• creates a HTML for a subset of variants based on config. Shows read context and fragment support
• config 'vis_variants' to specify variants to produce visualisations, format: 'chromosome:position:ref:alt' separated by ';'. Will only run sage for +/- 200 base region around specified variants.
• config 'vis_pass_only' to generate files for passing variants, must be called with 'specific_regions'
• config 'vis_output_dir' default 'vis' if not specified

Config:

• sync_fragments removed since now on by default. Use 'no_fragment_sync' to disable.
• output -> output_vcf