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v0.2.7

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

v0.2.6

  • fix name collisions with cram (#134)

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.

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 (arq5x/lumpy-sv#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.

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 @davemcg for feedback on this feature).

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)

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.

v0.2.0

  • add duphold annotations. (requires duphold v0.0.4)

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

v0.1.10

  • fix type in annotate (s/Number/Integer/)

v0.1.9

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

v0.1.8

  • don't use --sum in merge step. this reduces the size of CI when using smoove merge

v0.1.7

  • add a SHQ: smoove het-quality score to the FORMAT field and a MSHQ:mean smoove het-quality score to the INFO. Variants with a het-quality of 4 are quite good.

v0.1.6

  • sensitivity improvement by dropping reads with > 5 mismatches.

v0.1.5

  • sensitivity increases for variants without split reads.
  • use a fixed length of 4 in merge (gives much better merging)
  • 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.

v0.1.4

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

v0.1.3

  • update command to match latest mosdepth

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