smoove - allow setting max depth

previously regions with > 1000 depth were filtered out. That can now be set with an environment variable:

export SMOOVE_MAX_DEPTH=20000 smoove call ...

- Go
Published by brentp almost 5 years ago

smoove - larger chroms, more samples

as of this release, the argument to smoove paste can be a file ending with .list that has one file per sample.

v0.2.7

use csi index for bams to support larger organisms
fix ordering of error-checking (#146)
support for longer file-lists (#151)

- Go
Published by brentp about 5 years ago

v0.2.6

fix name collisions with cram (#134)

- Go
Published by brentp over 5 years ago

smoove - shorten run-time for problematic samples

v0.2.5

slight sensitivity increase
fix bug in VCF parser that could manifest inside of smoove annotate
reduce run time for problematic samples. using a kdtree.
@brwnj fixed the docker container so that conversion to singularity works without futzing.

- Go
Published by brentp over 6 years ago

v0.2.4

add ##reference=$fasta to vcf header. (#58)
fix smoove annotate for recent ensembl GFFs which lack transcript features
fix bug in lumpy_filter for some versions of GCC (https://github.com/arq5x/lumpy-sv/pull/300)
just report message on weird alignments instead of failing (#68)
lower lumpy z cutoff from 4 to 2.75. because of distribution of fragment lengths, this does not affect much, but does improve sensitivity after duphold-DHFFC filtering slightly.

- Go
Published by brentp almost 7 years ago

smoove - diagnostics and lower FPR

v0.2.3

save disc and split counts and output a plot as QC
annotate: annotate with up and downstream 5KB. so any gene within 5kb will be annotated.
smoove merge now outputs a plot that shows the number of split and discordant reads for each sample.
smoove now filters about 25% more split reads by looking at how the read is consumed this results in a 5% reduction in false positive genome-in-a-bottle deletions > 1KB while leaving the true positives unchanged relative to version 0.2.2. (Thanks @ernfrid for feedback on this feature).

- Go
Published by brentp over 7 years ago

smoove -

NOTE that this release requires a very recent version of mosdepth

v0.2.2

huge reduction in number of discordant reads sent to lumpy for some problematic samples. this is work by @ernfrid which reduces lumpy runtime for all cases and dramatically lowers it for cases that were previously problematic due to large numbers of discordant reads. On our Genome in a Bottle test sample, this drops the number of discordant reads from 1,434,810 to 332,384; a 4.3 fold reduction while leaving the final smoove output unchanged except for 2 BNDs that were removed. This reduction in reads will be even more dramatic in problematic samples.
switch to use svtyper>=0.7.0 with --max_ci_dist parameter. To avoid this set: export SMOOVE_NO_MAX_CI=xx # any value will work; however, it's higly recommended to use as-is.
cnvnator changes and filtering. (still requires github.com/brentp/CNVnator fork).
bugfix for case when no output directory was specified.
use mosdepth with --fast-mode NOTE this requires the latest version of mosdepth (0.2.4 or greater)

- Go
Published by brentp over 7 years ago

smoove - general improvements in sensitivity for small events

this release was driven by feedback from Dave Larson (@ernfrid) and Ira Hall's group. It results in improved sensitivity for smaller events (at a small cost of specificity). It also fixes a bug with the duphold runner.

v0.2.1

fix bug in smoove duphold for samples > threads that resulted in stalling
smoove is now more discerning about reads that are soft-clipped on both ends as these could be due to inversions. if a read is not flipped relative to its mate and it is soft-clipped on both ends, it is still removed.
in some cases reads with a large NM (mismatches) were not filtered because they had an unexpected type (uint8). smoove now checks more types and for some bams will remove more records which improves specificity.
smoove will now be more conservative with NM counting. an insertion of 7 bases is counted as an NM of 7. smoove will now correct this to an NM of 1 so it counts the number of events rather than the number of bases of each event.
simplify rules for filtering and make them less strict.

- Go
Published by brentp over 7 years ago

smoove -

v0.2.0

add duphold annotations. (requires duphold v0.0.5 or higher)

v0.1.11

flip start and end for small percent of cases where that's a problem
expose min sample weight to allow adjusting required support for each variant

- Go
Published by brentp over 7 years ago

smoove - s/Number/Integer/

the type of SHQ and MSHQ was invalid in previous versions that is fixed in this release.

- Go
Published by brentp almost 8 years ago