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igmmbioinformatics
trio-whole-exome
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3a2520e2
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3a2520e2
authored
3 years ago
by
ameyner2
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Update tool_and_data_change_tracking.md
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Ultra 2 SOP/doc updates
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3a2520e2
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
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