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feat: Add results for sarek 3.4.4 #48

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feat: Add results for sarek 3.4.4 #48

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173 changes: 144 additions & 29 deletions config/config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,7 @@ variant-calls:
zenodo:
deposition: 7734757
filename: cropbioBonn_WGGC_WES_BO_Twist.vcf.gz
benchmark: giab-NA12878-twist
benchmark: giab-NA12878-twist
CO-agilent-200M:
labels:
site: cologne
Expand Down Expand Up @@ -195,7 +195,7 @@ variant-calls:
subcategory: CHM-eval
zenodo:
deposition: 7352532
filename: ERR1341796_bwa.deepvariant.vcf.gz
filename: ERR1341796_bwa.deepvariant.vcf.gz
benchmark: chm-eval
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
GHGA-sarek-bwa-strelka-CHM-ERR1341796:
Expand All @@ -206,7 +206,7 @@ variant-calls:
subcategory: CHM-eval
zenodo:
deposition: 7352532
filename: ERR1341796_bwa.strelka.variants.vcf.gz
filename: ERR1341796_bwa.strelka.variants.vcf.gz
benchmark: chm-eval
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
# TODO add again after technical issues have been fixed: callset is empty!
Expand Down Expand Up @@ -240,7 +240,7 @@ variant-calls:
subcategory: CHM-eval
zenodo:
deposition: 7352532
filename: ERR1341796_bwa_bcftools_mpileup.vcf.gz
filename: ERR1341796_bwa_bcftools_mpileup.vcf.gz
benchmark: chm-eval
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
GHGA-sarek-dragmap-deepvariant-CHM-ERR1341796:
Expand All @@ -251,7 +251,7 @@ variant-calls:
subcategory: CHM-eval
zenodo:
deposition: 7352532
filename: ERR1341796_dragmap.deepvariant.vcf.gz
filename: ERR1341796_dragmap.deepvariant.vcf.gz
benchmark: chm-eval
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
GHGA-sarek-dragmap-strelka-CHM-ERR1341796:
Expand All @@ -262,7 +262,7 @@ variant-calls:
subcategory: CHM-eval
zenodo:
deposition: 7352532
filename: ERR1341796_dragmap.strelka.variants.vcf.gz
filename: ERR1341796_dragmap.strelka.variants.vcf.gz
benchmark: chm-eval
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
GHGA-sarek-dragmap-freebayes-CHM-ERR1341796:
Expand All @@ -273,7 +273,7 @@ variant-calls:
subcategory: CHM-eval
zenodo:
deposition: 7352532
filename: ERR1341796_dragmap.freebayes.vcf.gz
filename: ERR1341796_dragmap.freebayes.vcf.gz
benchmark: chm-eval
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
GHGA-sarek-dragmap-haplotypecaller-CHM-ERR1341796:
Expand All @@ -284,10 +284,9 @@ variant-calls:
subcategory: CHM-eval
zenodo:
deposition: 7352532
filename: ERR1341796_dragmap.haplotypecaller.filtered.vcf.gz
filename: ERR1341796_dragmap.haplotypecaller.filtered.vcf.gz
benchmark: chm-eval
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt

TB-sarek27-freebayes-agilent-200M:
labels:
site: TB QBiC
Expand All @@ -305,7 +304,6 @@ variant-calls:
filename: WES_high_coverage_FreeBayes_NA12878.vcf.gz
benchmark: giab-NA12878-agilent-200M
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt

TB-sarek27-haplotypecaller-agilent-200M:
labels:
site: TB QBiC
Expand All @@ -323,7 +321,6 @@ variant-calls:
filename: WES_high_coverage_HaplotypeCaller_NA12878.vcf.gz
benchmark: giab-NA12878-agilent-200M
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt

TB-sarek27-strelka-agilent-200M:
labels:
site: TB QBiC
Expand All @@ -341,7 +338,6 @@ variant-calls:
filename: WES_high_coverage_Strelka_NA12878_variants.vcf.gz
benchmark: giab-NA12878-agilent-200M
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt

TB-sarek27-freebayes-agilent-75M:
labels:
site: TB QBiC
Expand All @@ -359,7 +355,6 @@ variant-calls:
filename: WES_low_coverage_FreeBayes_NA12878.vcf.gz
benchmark: giab-NA12878-agilent-75M
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt

TB-sarek27-haplotypecaller-agilent-75M:
labels:
site: TB QBiC
Expand All @@ -377,7 +372,6 @@ variant-calls:
filename: WES_low_coverage_HaplotypeCaller_NA12878.vcf.gz
benchmark: giab-NA12878-agilent-75M
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt

TB-sarek27-strelka-agilent-75M:
labels:
site: TB QBiC
Expand All @@ -395,7 +389,6 @@ variant-calls:
filename: WES_low_coverage_Strelka_NA12878_variants.vcf.gz
benchmark: giab-NA12878-agilent-75M
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt

TB-sarek311-freebayes-agilent-200M:
labels:
site: TB QBiC
Expand All @@ -413,7 +406,6 @@ variant-calls:
filename: WES_agilent_high_cov_sarek311_NA12878_freebayes.vcf.gz
benchmark: giab-NA12878-agilent-200M
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt

TB-sarek311-haplotypecaller-agilent-200M:
labels:
site: TB QBiC
Expand All @@ -431,7 +423,6 @@ variant-calls:
filename: WES_agilent_high_cov_sarek311_NA12878_haplotypecaller.vcf.gz
benchmark: giab-NA12878-agilent-200M
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt

TB-sarek311-strelka-agilent-200M:
labels:
site: TB QBiC
Expand All @@ -449,7 +440,6 @@ variant-calls:
filename: WES_agilent_high_cov_sarek311_NA12878_strelka.vcf.gz
benchmark: giab-NA12878-agilent-200M
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt

TB-sarek311-freebayes-agilent-75M:
labels:
site: TB QBiC
Expand All @@ -467,7 +457,6 @@ variant-calls:
filename: WES_agilent_low_cov_sarek311_NA12878_freebayes.vcf.gz
benchmark: giab-NA12878-agilent-75M
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt

TB-sarek311-haplotypecaller-agilent-75M:
labels:
site: TB QBiC
Expand All @@ -485,7 +474,6 @@ variant-calls:
filename: WES_agilent_low_cov_sarek311_NA12878_haplotypecaller.vcf.gz
benchmark: giab-NA12878-agilent-75M
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt

TB-sarek311-strelka-agilent-75M:
labels:
site: TB QBiC
Expand All @@ -503,7 +491,6 @@ variant-calls:
filename: WES_agilent_low_cov_sarek311_NA12878_strelka.vcf.gz
benchmark: giab-NA12878-agilent-75M
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt

TB-sarek311-freebayes-twist:
labels:
site: TB QBiC
Expand All @@ -520,7 +507,6 @@ variant-calls:
filename: WES_twist_sarek311_NA12878_freebayes.vcf.gz
benchmark: giab-NA12878-twist
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt

TB-sarek311-haplotypecaller-twist:
labels:
site: TB QBiC
Expand All @@ -537,7 +523,6 @@ variant-calls:
filename: WES_twist_sarek311_NA12878_haplotypecaller.vcf.gz
benchmark: giab-NA12878-twist
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt

TB-sarek311-strelka-twist:
labels:
site: TB QBiC
Expand All @@ -554,7 +539,6 @@ variant-calls:
filename: WES_twist_sarek311_NA12878_strelka.vcf.gz
benchmark: giab-NA12878-twist
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt

DUE-varlociraptor:
zenodo:
deposition: 6396505
Expand Down Expand Up @@ -590,7 +574,6 @@ variant-calls:
filename: NA12878x2_76_var.vcf.gz
benchmark: giab-NA12878-agilent-200M
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt

TB-IMGAG-megSAP-freebayes-highsensitivity-agilent-75M:
labels:
site: TB - IMGAG
Expand All @@ -609,7 +592,6 @@ variant-calls:
filename: NA12878x2_77_var.vcf.gz
benchmark: giab-NA12878-agilent-75M
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt

TB-IMGAG-megSAP-freebayes-highsensitivity-twist:
labels:
site: TB - IMGAG
Expand All @@ -627,7 +609,142 @@ variant-calls:
filename: NA12878x2_78_var.vcf.gz
benchmark: giab-NA12878-twist
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt

nf-core-sarek-344-strelka2-agilent-75M:
labels:
site: nf-core
pipeline: nf-core/sarek v3.4.4
trimming: FastP v0.23.4
read-mapping: bwa mem v
base-quality-recalibration: gatk4 v4.5.0.0
realignment: none
variant-detection: strelka2 v2.9.10
genotyping: none
reads: 75M
subcategory: NA12878-agilent
zenodo:
deposition: 13742023
filename: NA12878_75M.strelka.variants.vcf.gzNA12878_75M.strelka.variants.vcf.gz
benchmark: giab-NA12878-agilent-75M
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
nf-core-sarek-344-deepvariant-agilent-75M:
labels:
site: nf-core
pipeline: nf-core/sarek v3.4.4
trimming: FastP v0.23.4
read-mapping: bwa mem v
base-quality-recalibration: gatk4 v4.5.0.0
realignment: none
variant-detection: deepvariant v1.5.0
genotyping: none
reads: 75M
subcategory: NA12878-agilent
zenodo:
deposition: 13742023
filename: NA12878_75M.deepvariant.vcf.gzNA12878_75M.deepvariant.vcf.gz
benchmark: giab-NA12878-agilent-75M
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
nf-core-sarek-344-freebayes-agilent-75M:
labels:
site: nf-core
pipeline: nf-core/sarek v3.4.4
trimming: FastP v0.23.4
read-mapping: bwa mem v
base-quality-recalibration: gatk4 v4.5.0.0
realignment: none
variant-detection: freebayes v1.3.6
genotyping: none
reads: 75M
subcategory: NA12878-agilent
zenodo:
deposition: 13742023
filename: NA12878_75M.freebayes.vcf.gzNA12878_75M.freebayes.vcf.gz
benchmark: giab-NA12878-agilent-75M
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
nf-core-sarek-344-haplotypecaller-agilent-75M:
labels:
site: nf-core
pipeline: nf-core/sarek v3.4.4
trimming: FastP v0.23.4
read-mapping: bwa mem v
base-quality-recalibration: gatk4 v4.5.0.0
realignment: none
variant-detection: haplotypecaller v4.5.0.0
genotyping: none
reads: 75M
subcategory: NA12878-agilent
zenodo:
deposition: 13742023
filename: NA12878_75M.haplotypecaller.filtered.vcf.gzNA12878_75M.haplotypecaller.filtered.vcf.gz
benchmark: giab-NA12878-agilent-75M
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
nf-core-sarek-344-strelka2-agilent-200M:
labels:
site: nf-core
pipeline: nf-core/sarek v3.4.4
trimming: FastP v0.23.4
read-mapping: bwa mem v
base-quality-recalibration: gatk4 v4.5.0.0
realignment: none
variant-detection: strelka2 v2.9.10
genotyping: none
reads: 200M
subcategory: NA12878-agilent
zenodo:
deposition: 13742023
filename: NA12878_200M.strelka.variants.vcf.gzNA12878_200M.strelka.variants.vcf.gz
benchmark: giab-NA12878-agilent-200M
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
nf-core-sarek-344-deepvariant-agilent-200M:
labels:
site: nf-core
pipeline: nf-core/sarek v3.4.4
trimming: FastP v0.23.4
read-mapping: bwa mem v
base-quality-recalibration: gatk4 v4.5.0.0
realignment: none
variant-detection: deepvariant v1.5.0
genotyping: none
reads: 200M
subcategory: NA12878-agilent
zenodo:
deposition: 13742023
filename: NA12878_200M.deepvariant.vcf.gzNA12878_200M.deepvariant.vcf.gz
benchmark: giab-NA12878-agilent-200M
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
nf-core-sarek-344-freebayes-agilent-200M:
labels:
site: nf-core
pipeline: nf-core/sarek v3.4.4
trimming: FastP v0.23.4
read-mapping: bwa mem v
base-quality-recalibration: gatk4 v4.5.0.0
realignment: none
variant-detection: freebayes v1.3.6
genotyping: none
reads: 200M
subcategory: NA12878-agilent
zenodo:
deposition: 13742023
filename: NA12878_200M.freebayes.vcf.gzNA12878_200M.freebayes.vcf.gz
benchmark: giab-NA12878-agilent-200M
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
nf-core-sarek-344-haplotypecaller-agilent-200M:
labels:
site: nf-core
pipeline: nf-core/sarek v3.4.4
trimming: FastP v0.23.4
read-mapping: bwa mem v
base-quality-recalibration: gatk4 v4.5.0.0
realignment: none
variant-detection: haplotypecaller v4.5.0.0
genotyping: none
reads: 200M
subcategory: NA12878-agilent
zenodo:
deposition: 13742023
filename: NA12878_200M.haplotypecaller.filtered.vcf.gzNA12878_200M.haplotypecaller.filtered.vcf.gz
benchmark: giab-NA12878-agilent-200M
rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
custom-benchmarks:
giab-NA12878-agilent-200M:
zenodo:
Expand Down Expand Up @@ -656,8 +773,6 @@ custom-benchmarks:
- resources/zenodo/custom-benchmarks/giab-NA12878-twist/NA12878_HG001_Twist_Bonn_2.fq.gz
target-regions: resources/https/www.twistbioscience.com/sites/default/files/resources/2022-01/Twist_Comprehensive_Exome_Covered_Targets_hg38.bed
grch37: false

limit-regions:
activate: false

grch37: false
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