v2.8.0

• Added ExomeDepth

v2.7.1

• Temporary add ExonCov v3 (Optional INI setting)

v2.7.0

• GATK > 3.8
• BAF plot update, see #118

v2.6.1

• Add stand_emit_conf and stand_call_conf to genotype gvcf step.
• Add CHECKING_CLEANUP script step.
• Make Base Recalibration QC optional.
• Check if input_vcf exists before starting single sample vcf step.

v2.6.0

Changes:

• Implement Hartwig IAP 1.12 changes. #99
• New SOMATIC_REGEX_REF_CODE and SOMATIC_REGEX_TUMOR_CODE settings to make somatic sample parsing more versatile.
• Add INS calling for DELLY. #101
• Update bcftools to fix roh analysis. #103
• Set output dir for Exoncov instead of using default. #84
• Fix bug in makeKaryotype.R . #96
• Delly now checks final output. #104

v2.5.1

Changes:

• GATK VariantFilter: Unique names for indel and snp filters.

v2.5.0

New features:

• IAP modules in own namespace.
• Initial implementation of bcftools roh
• Sync IAP with Harwtig Pipeline v1.10 and v1.11
  • Add VT normalize to freebayes analysis.
  • Update freebayes filter script.
  • Update somatic melt script.
  • Check fastq.gz pattern before submitting jobs.
• Fingerprint module
• Single sample vcf output optional in vcf utils

Bug fixes:

• Allow only one mappability track in freec analysis
• Add --temporary-directory to vcf-sort in delly analysis, fix #95

v2.4.1

Changes:

• Add recalibrated bams to checking_rm list
• Set correct cluster_project for kg ini

v2.4.0

New features:

• QDNAseq support
• Add MIT license
• Add CHECKING_RM setting

Other / bug fixes:

• Hartwig v1.9 changes
• BAF module fix for complex (somatic) samples
• Upgrade to sambamba v0.6.5

v2.3.0

New features:

• Sex aware variant calling + new haplotypecaller scala script -> add CALLING_SEXAWARE to ini
• Using relative paths for qscripts and IAP scripts
• Save submission log automatically
• Add flagstat stats to bamMetrics -> needs new version of bamMetrics

Bug fixes:

• Delly job submission
• Delly chromosome chunks