fastq-tools v1.0.0-beta.1

Initial release of biomodal fastq collapse component.

To run this component use:

java -cp fastq-tools-v1.0.0-beta.1.jar com.hartwig.hmftools.fastqtools.biomodalcollapse.BiomodalCollapse \
  -threads $NUMBER_OF_THREADS \
  -fastq1 $PATH_TO_R1_FASTQ \
  -fastq2 $PATH_TO_R2_FASTQ \
  -out_fastq $COLLAPSED_FASTQ_OUTPUT_PATH

Note that you can restrict the tool to only process the first $N fragments by adding the argument -max_fastq_pairs_read $N to the above.

compar v1.3.0-beta.3

Description of release compar v1.3.0-beta.3

DEV-3784: Add liftover for somatic disruptions and germline variants and disruptions.
Make compatible with Cuppa v2.
DEV-4061: Add many fields and new categories: PEACH, VIRUS, TUMOR_FLAGSTAT, GERMLINE_FLAGSTAT, TUMOR_BAM_METRICS, GERMLINE_BAM_METRICS, SNP_GENOTYPE.
Removed support for old format germline SV file.
Adjusted disruption comparison to be less dependent on exact position.
DEV-4082: Create INVALID_ERROR output when error is thrown in comparison
DEV-4084: Fix problems in disruption comparison
Add categories: CDR3_SEQUENCE, CDR3_LOCUS_SUMMARY, TELOMERE_LENGTH

Full Changelog: compar-v1.2...compar-v1.3.0-beta.3

virus-interpreter v3.7-beta.4

Description of release virus-interpreter v3.7-beta.4

What's Changed

• ACTIN-346: Derive 5 breakend fields from root sources in ORANGE by @kzuberihmf in #620

Full Changelog: orange-v3.7.1_beta...virus-interpreter-v3.7-beta.4

virus-interpreter v3.7-beta.3

Description of release virus-interpreter v3.7-beta.3

What's Changed

• ACTIN-346: Derive 5 breakend fields from root sources in ORANGE by @kzuberihmf in #620

Full Changelog: orange-v3.7.1_beta...virus-interpreter-v3.7-beta.3

virus-interpreter v3.7-beta.2

Description of release virus-interpreter v3.7-beta.2

What's Changed

• ACTIN-346: Derive 5 breakend fields from root sources in ORANGE by @kzuberihmf in #620

Full Changelog: orange-v3.7.1_beta...virus-interpreter-v3.7-beta.2

v-chord v0.1_beta.1

Description of release v-chord v0.1_beta.1

Full Changelog: compar-v1.3.0-beta.2...v-chord-v0.1_beta.1

compar v1.3.0-beta.2

Description of release compar v1.3.0-beta.2

What's Changed

DEV-3784: Add liftover for somatic disruptions and germline variants and disruptions.
Make compatible with Cuppa v2.
DEV-4061: Add many fields and new categories: PEACH, VIRUS, TUMOR_FLAGSTAT, GERMLINE_FLAGSTAT, TUMOR_BAM_METRICS, GERMLINE_BAM_METRICS, SNP_GENOTYPE.
Removed support for old format germline SV file.
Adjusted disruption comparison to be less dependent on exact position.
DEV-4082: Create INVALID_ERROR output when error is thrown in comparison
DEV-4084: Fix problems in disruption comparison
Add categories: CDR3_SEQUENCE, CDR3_LOCUS_SUMMARY, TELOMERE_LENGTH

Full Changelog: compar-v1.2...compar-v1.3.0-beta.2

orange v3.7.1_beta

Description of release orange v3.7.1_beta

What's Changed

• ACTIN-292: Add Chromosomal Rearrangements by @cbruel in #612
• DEV-4083: Incorporate biallelic probability in Orange by @DFKoetsier in #615
• Fix crashing on samples containing no data (e.g. no template controls (NTC))

Full Changelog: cuppa-v2.3.0_beta...orange-v3.7.1_beta

chord v2.1.0 beta

Beta 0:

• Reimplemented mutSigExtractor R package in java

Beta 1:

• Replace CHORD R package with an R script and java wrapper
• Exclude variants where FILTER is '.' when selecting PASS variants

Beta 2:

• Fix ChordDataPrep not working on hg38 by storing chromosomes from VCF as String rather than HumanChromosome

cuppa v2.3 beta

Beta 0:

• Use latest SV factory

Beta 1:

• Fix misalignment of cancer type columns in visualization heatmap