Tools upgrade on bcbio

docs/tool_and_data_change_tracking.md

-Software | bcbio-1.1.5 (ultra) | bcbio-1.2.3 (ultra) | bcbio-1.2.8 (ultra2) | Notes
----------|-------------|-------------|-------------|------
-bcbio-nextgen | 1.1.5-b | **1.2.3** | **1.2.8** | Pipeline
-bcftools | 1.9 | **1.10.2** | **1.9** | VCF manipulation suite
-gatk4 | 4.1.2.0 | **4.1.8.1** | **4.2.1.0** | Alignment post-processing and variant calling
-picard | 2.20.5 | **2.23.3** | **2.25.7** | VCF/BAM manipulation suite - only one VCF tool used
-samtools | 1.9 | 1.9 | 1.9 | 
-variant-effect-predictor | 97.3 | **100.4** | 100.4 | VCF annotations
-bamtools | 2.4.0 | 2.4.0 | 2.4.0 |
-bcbio-variation | 0.2.6 | 0.2.6 | 0.2.6 | 
-bedtools | 2.27.1 | 2.27.1 | **2.30.0** | BED file manipulation suite
-biobambam | 2.0.87 | 2.0.87 | 2.0.87 | 
-bwa | 0.7.17 | 0.7.17 | 0.7.17 | 
-fastqc | 0.11.8 | 0.11.8 | 0.11.8 | 
-grabix | 0.1.8 | 0.1.8 | 0.1.8 | 
-vt | 2015.11.10 | 2015.11.10 | 2015.11.10 | 
-vase | 0.2.4 | **0.4** | **0.4.2** | Identification of de novo variants
-rtg-tools | 3.10.1 | **3.11** | 3.11 | Used for GIAB concordance analysis
+Software | bcbio-1.1.5 (ultra) | bcbio-1.2.3 (ultra) | bcbio-1.2.8 (ultra2) | bcbio-1.2.8 (ultra2 tools upgrade) | Notes
+---------|-------------|-------------|-------------|------|-------
+bcbio-nextgen | 1.1.5-b | **1.2.3** | **1.2.8** | 1.2.8 | Pipeline
+bcftools | 1.9 | **1.10.2** | **1.9** | **1.13** | VCF manipulation suite
+gatk4 | 4.1.2.0 | **4.1.8.1** | **4.2.1.0** | **4.2.5.0** | Alignment post-processing and variant calling
+picard | 2.20.5 | **2.23.3** | **2.25.7** | **2.26.10** | VCF/BAM manipulation suite - only one VCF tool used
+samtools | 1.9 | 1.9 | 1.9 | **1.7** | BAM manipulation suite 
+variant-effect-predictor | 97.3 | **100.4** | 100.4 | 100.4 | VCF annotations
+bamtools | 2.4.0 | 2.4.0 | 2.4.0 | 2.5.1 | BAM manipulation suite
+bcbio-variation | 0.2.6 | 0.2.6 | 0.2.6 | 0.2.6 
+bedtools | 2.27.1 | 2.27.1 | **2.30.0** | 2.30.0 | BED file manipulation suite
+biobambam | 2.0.87 | 2.0.87 | 2.0.87 | **2.0.182** | BAM manipulation suite
+bwa | 0.7.17 | 0.7.17 | 0.7.17 | 0.7.17 
+fastqc | 0.11.8 | 0.11.8 | 0.11.8 | **0.11.9** | QC checks on FASTQ files
+grabix | 0.1.8 | 0.1.8 | 0.1.8 | 0.1.8 |
+vt | 2015.11.10 | 2015.11.10 | 2015.11.10 | 2015.11.10 |
+vase | 0.2.4 | **0.4** | **0.4.2** | 0.4.2 | Identification of de novo variants
+rtg-tools | 3.10.1 | **3.11** | 3.11 | **3.12.1** | Used for GIAB concordance analysis
 
 Resource | bcbio-1.1.5 (ultra) | bcbio-1.2.3 (ultra) | bcbio-1.2.8 (ultra2) | Notes
 ---------|-------------|-------------|-------------|------