sage v3.1

Functional:

• lowered event penalty from 8 to 7
• count realigned reads towards tumor qual
• test realignment at left and right core only
• only realign INDELs >= 3 bases or with an INDEL in read overlapping the variant core
• add 1 to realign max distance
• find inserts in soft-clipped bases, minimum length of 12 and at least 5 bases from start of soft-clip, use supplementary reads
• add separate soft-filters for minGermlineCoverage (9 and 15, vs existing 6 and 10) for inserts of at least 10 bases
• added evidence core search to see if straddles the soft-clip and matched region
• use avg base-qual for raw alt quality for indels
• allow core low base-qual matching for inserts at a rate of 1 per 20 inserted bases
• added hotspot min raw alt base quality threshold of 150
• max alt support now also applied to inserts >= 10 bases and as a percent vs 1%

Bugs:

• fixed indel dedup where multiple overlap

Technical:

• write multiple local phase sets to VCF
• handle x.y.z type versions when checked in append mode