more error handling

v0.1.9

• better error message in merge.
• use set -e in process calls so we don't exit with 0 even on failure

no --sum in smoove merge

this release will slightly improve sensitivity when using smoove in cohort mode.

variant prioritization and quality

The smoove annotate command now adds a SHQ (Smoove Het Quality) tag to every sample format) a value of 4 is a high quality call and the value of 1 is low quality. -1 is non-het.
It also adds a MSHQ for Mean SHQ to the INFO field which is the mean SHQ score across all heterozygous samples for that variant.

As a first pass, users can look for variants with MSHQ > 3.

This value is created from a data-driven model of het quality trained on 603 samples in large pedigrees and on > 500 quartets.

specificity improvements

found a read filter that removes about 30% of false-positive calls in a test-case using the CHM1/CHM13 pseudo-diploid.

sensitivity improvements

NOTE: there is a change to svtyper that we found in evaluating smoove that will reduce the FPR from genotyping. Please update to svtyper>0.6.0 for best results.

v0.1.5

• sensitivity increases for variants without split reads.
• use a fixed length of 4 in merge (gives much better merging for smoove merge)
• add new annotate command which takes a gff and annotates with gene names
• increase max_reads argument to svtyper to reduce false negatives
• remove QCFail and duplicate reads from split and disc.bams. This is now
  part of smoove but also fixed in lumpy_filter upstream.

fix for --removepr

v0.1.4

• fix bug when using -x/--removepr with --genotype (thanks @chapmanb for test-case)

mosdepth compat

the only change compared to v0.1.2 is to support the most recent mosdepth output (previous versions of mosdepth will also work with this version).

usability changes

v0.1.2

• bcftools and gsort are now required.
• output never goes to STDOUT
• output contigs to header
• add svtools to docker
• add option to remove PRPOS and PREND

initial release

v0.1.1

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