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Changelog

v0.34

  • Fixing problem with left-trimming variants (#99).

v0.33

  • Fixing bug triggered for GRCh38 without chr prefix (#98).

v0.32

  • Fixing bug when annotating MELT with missing AD (#95).

v0.31

  • Interpret FORMAT/SQ as Float (#93).

v0.30

  • Adding support for MELT (#91).

v0.29

  • Fix with merging SV annotation files from Delly2 SV (#88).

v0.28

  • Write out FORMAT/SQ in the case that is present and FORMAT/GQ is not (#84). If neither is set, then write out 0. Write out 0 for AD and DP as well if missing. This improves compatibility with DRAGEN.
  • Suppress BND records that point to non-allow-listed contigs (#85). This is required for processing Manta and Delly2 results, for example.

v0.27

IMPORTANT COMPATIBILITY NOTE: For annotating SVs, the output of this version is not compatible with varfish-server v1.2 (Anthenea) and early versions of the v2 (Bollonaster) development branch. You can generate compatible files by adding the --opt-out=chrom2-columns,dbcounts-columns,callers-array as arguments to annotate-svs.

  • Writing out proper SV type for Dragen CNV (#76)
  • Adding support for depth of coverage annotation (#73)
  • Ensure output files are sorted by chromosomes (#79)
  • Handle multiple input VCFs in annotate-svs with filtering (#75)
  • Write out SV callers as array (#81)

v0.26

  • Explicitely model support for SV callers (#68)
  • Removing explicit support for SV2 (#67)
  • Adding end-to-end tests hg19-chr22 (#61)

v0.25

  • Fixing unresolved issue with self-test (#51, #56)

v0.24

  • Fixing problem with self-test on gnomAD genomes with chrY (#51)
  • Suppress writing out *Carriers information in INFO column for SVs (#53)

v0.23

IMPORTANT COMPATIBILITY NOTE: For annotating SVs, the output of this version is not compatible with varfish-server v1.2 (Anthenea) and early versions of the v2 (Bollonaster) development branch. You can generate compatible files by adding the --opt-out=chrom2-columns,dbcounts-columns as arguments to annotate-svs.

  • Adding chrom2/count columns to output of annotate-sv (#41)
  • Writing out BND mates for Delly (#45)

v0.22

  • Adding db-stats command (#25)
  • Adding issue templates (#28)
  • Adding continuous integration with GitHub Actions (#28)
  • Adding unit tests for annotate command (#31)
  • Adding unit tests for annotate-sv command (#33)
  • Writing out gzip-ed files if output file name ends in .gz (#11)
  • Do not write out asterisk alleles (#18)
  • Adding tests for GRCh38 (#22)
  • Adding self-tests for annotation (#27)
  • Allow properly counting hemizygous variants when pedigree file is given (#36)

v0.21

  • Bumping jannovar-core dependency for fixes in chrMT annotation.

v0.20

  • Further bumping of jannovar-core against log4shell.
  • Fixing problem with missing SVMETHOD annotation of SV VCFs.

v0.19

  • Bumping jannovar-core dependencies against log4shell vulnerability.

v0.18

  • Fixing problems with querying in GRCh38.

v0.17

  • Adding support for GRCh38 release.

v0.16

  • Fixing import of ExAC r1 VCF.
  • Prevent import of REF and ALT alleles with sizes above 1000bp (field lengths in database).

v0.15

  • Properly removing "chr" prefix for data aligned to hg19.
  • Checking whether the supported release GRCh37/hg19 was used. Will only allow processing of such genomes and block variants from GRCh38/hg38 which would lead to incorrect results.

v0.14

  • Bumping junit and guava dependency.
  • Make compatible with new clinvar TSV file.

v0.13

  • Bumping HTSJDK dependency.
  • Fixing issue with empty "AD" fields.

v0.12

  • Removing CNVetti::homdel support as it was a dead end.
  • Fixing gCNV support.

v0.11

  • Adding support for gCNV output.
  • Adding support for CNVetti::homdel output.

v0.10

  • Bumping Jannovar dependency (adds annotation of chrMT).
  • Writing out distance to refseq/ensembl exon and adding placeholder for info field.
  • Reading of updated clinvar and HGMD Public TSV.

v0.9

  • Writing out case and set ID into all output tables.
  • Fixing clinvar import into database.
  • Initializing case and set ID parameters to ".".

v0.8

  • Adding chromosome_no output column.

v0.7

  • Bumping Jannovar dependency to v0.32.
  • Refactoring columns of small and structural variant call file.
  • Not writing out variant effects for small variants any more.
  • Writing out overall allele frequency and not AF_POPMAX any more. This requires rebuilding the VarFish annotator database.
  • Replacing pos and pos_end in database by start and end to make it consistent with created files.
  • Properly matching variants by gene without duplicates (#6).

v0.6

  • Adding support for XHMM GT attributes.

v0.5

  • Bumping Jannovar dependency (properly load SV type from SV2 output).
  • Reading out FORMAT fields from SV2 output.

v0.4

  • Fixing bug that gave wrong paired read reference counts.
  • BNDs are not annotated as linear variants any more, instead: start == end.

v0.3

  • Improved annotation of Delly2 output.

v0.2

  • Fixing bug that prevented intergenic variants from being written out. Now, intergenic variatns are written out properly.

v0.1

  • Everything is new.