From 3a2520e274cf6c6521dbd3d6b70807e881650c6b Mon Sep 17 00:00:00 2001 From: ameyner2 <alison.meynert@ed.ac.uk> Date: Thu, 18 Nov 2021 08:15:08 +0000 Subject: [PATCH] Update tool_and_data_change_tracking.md --- docs/tool_and_data_change_tracking.md | 28 +++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/docs/tool_and_data_change_tracking.md b/docs/tool_and_data_change_tracking.md index a3377e2..614a063 100644 --- a/docs/tool_and_data_change_tracking.md +++ b/docs/tool_and_data_change_tracking.md @@ -1,21 +1,21 @@ 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 +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 | +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 +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 +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 Resource | bcbio-1.1.5 (ultra) | bcbio-1.2.3 (ultra) | bcbio-1.2.8 (ultra2) | Notes ---------|-------------|-------------|-------------|------ @@ -25,20 +25,20 @@ ccds | r20 | r20 | r20 | capture_regions | 20161202 | 20161202 | 20161202 | coverage | 2018-10-16 | 2018-10-16 | 2018-10-16 | prioritize | 20181227 | 20181227 | 20181227 | -dbsnp | 151-20180418 | 153-20180725 | 154-20210112 | VCF annotations +dbsnp | 151-20180418 | **153-20180725** | **154-20210112** | VCF annotations hapmap_snps | 20160105 | 20160105 | 20160105 | 1000g_omni_snps | 20160105 | 20160105 | 20160105 | ACMG56_genes | 20160726 | 20160726 | 20160726 | 1000g_snps | 20160105 | 20160105 | 20160105 | mills_indels | 20160105 | 20160105 | 20160105 | 1000g_indels | 2.8_hg38_20150522 | 2.8_hg38_20150522 | 2.8_hg38_20150522 | -clinvar | 20190513 | 20190513 | 20210110 | VCF annotations +clinvar | 20190513 | 20190513 | **20210110** | VCF annotations, not used qsignature | 20160526 | 20160526 | 20160526 | genesplicer | 2004.04.03 | 2004.04.03 | 2004.04.03 | effects_transcript | 2017-03-16 | 2017-03-16 | 2017-03-16 | varpon | 20181105 | 20181105 | 20181105 | -vcfanno | 20190119 | 20190119 | 20210204 | VCF annotations +vcfanno | 20190119 | 20190119 | **20210204** | VCF annotations, not used viral | 2017.02.04 | 2017.02.04 | 2017.02.04 | -gnomad genomes | 2.1 | 3.0 | 3.1.1 | VCF annotations -gnomad exomes | 2.1 | 2.1 | 2.1.1 | VCF annotations +gnomad genomes | 2.1 | **3.0** | **3.1.1** | VCF annotations +gnomad exomes | 2.1 | 2.1 | **2.1.1** | VCF annotations dbnsfp | 3.5a | not installed | not installed | VCF annotations, not used -- GitLab