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2
votes
5
replies
2.0k
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GATK SelectVariants consider spanning/overlapping deletions as SNP
SelectVariants SNP gatk INDEL
updated 10 months ago by ▴ 210 • written 4.1 years ago by ▴ 290
2
votes
6
replies
2.3k
views
filter multisample VCF based on Altered AD values
vcf ad filter
updated 20 months ago by ▴ 10 • written 5.1 years ago by ▴ 290
3
votes
12
replies
5.6k
views
GATK Mutect2 tumor mode
gatk mutect2 tumor human wgs
updated 2.3 years ago by • 0 • written 4.8 years ago by ▴ 290
4
votes
0
replies
941
views
Tool: Visual analysis of VCF files
vcf visual-analysis
updated 2.5 years ago by 45k • written 2.5 years ago by ▴ 290
0
votes
0
replies
5.0k
views
Answer: Answer: Plot number of mutations in each cancer type in VCF files?
2.6 years ago by cocchi.e89 ▴ 290
0
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0
replies
3.7k
views
Answer: Answer: Mutational landscape plot from VCF files
2.6 years ago by cocchi.e89 ▴ 290
0
votes
0
replies
4.6k
views
Answer: Answer: plotting AF in vcf files
2.6 years ago by cocchi.e89 ▴ 290
1
vote
0
replies
9.0k
views
Answer: Answer: Making nice plots based on the different metrics from VCF file
2.6 years ago by cocchi.e89 ▴ 290
0
votes
0
replies
2.5k
views
Comment: Comment: hg38 low-quality site BED file
2.6 years ago by cocchi.e89 ▴ 290
0
votes
1
reply
2.5k
views
Comment: Comment: hg38 low-quality site BED file
2.6 years ago by cocchi.e89 ▴ 290
0
votes
1
reply
2.5k
views
Comment: Comment: hg38 low-quality site BED file
2.6 years ago by cocchi.e89 ▴ 290
4
votes
8
replies
2.5k
views
hg38 low-quality site BED file
human low-quality-site BED hg38
2.6 years ago by cocchi.e89 ▴ 290
3
votes
1
reply
1.3k
views
gene pLI score
gene loss-of-function pli
updated 2.9 years ago by 5.0k • written 2.9 years ago by ▴ 290
0
votes
0
replies
578
views
mosaic loss of chromosome - bioinformatics score
GATK chromosome CNV loss mosaic
2.9 years ago by cocchi.e89 ▴ 290
0
votes
1
reply
818
views
why Mutect2 calls some germline variants as somatic ones?
somatic germline haplotypecaller mutect2
updated 3.3 years ago by ★ 1.6k • written 3.3 years ago by ▴ 290
0
votes
2
replies
1.8k
views
extract gnomAD (exome/genome) all variant list in a specific gene (hg19)
gnomAD human hg19
updated 3.4 years ago by ▴ 50 • written 4.3 years ago by ▴ 290
0
votes
1
reply
788
views
Genome variants - regional distribution analysis
genome human variants distribution
updated 3.5 years ago by ★ 1.5k • written 3.5 years ago by ▴ 290
3
votes
2
replies
1.6k
views
VEP repeated region flag
VEP repeated-region variant human
updated 3.5 years ago by ▴ 60 • written 4.6 years ago by ▴ 290
0
votes
0
replies
633
views
updated in-silico scoring system for missense variants
pathogenicity missense in-silico
3.7 years ago by cocchi.e89 ▴ 290
1
vote
1
reply
1.5k
views
GenomicsDBImport from Mutect2 output
Mutect2 GenomicsDBImport somatic VCF GATK
updated 24 months ago by ▴ 110 • written 3.9 years ago by ▴ 290
0
votes
0
replies
7.9k
views
Comment: Comment: GATK genomicsDBimport intervals for WGS
3.9 years ago by cocchi.e89 ▴ 290
0
votes
0
replies
639
views
average variants number human WGS
variant WGS SNP INDEL
4.1 years ago by cocchi.e89 ▴ 290
0
votes
1
reply
2.0k
views
Comment: Comment: GATK SelectVariants consider spanning/overlapping deletions as SNP
4.1 years ago by cocchi.e89 ▴ 290
4
votes
9
replies
8.0k
views
GATK Mutect2 Panel-Of-Normals generation
gatk mutect2 panel-of-normal wes non-tumor
updated 4.2 years ago by • 0 • written 5.0 years ago by ▴ 290
0
votes
0
replies
1.4k
views
germline vs somatic CNV GATK calling
CNV germline somatic GATK WGS
4.2 years ago by cocchi.e89 ▴ 290
1
vote
1
reply
915
views
CWL input files as secondaryFiles JS
CWL input secondaryFiles
updated 3.9 years ago by ★ 1.9k • written 4.2 years ago by ▴ 290
1
vote
1
reply
1.0k
views
CWL workflow - nested_crossproduct output
CWL scatter workflow nested_crossproduct
updated 3.9 years ago by ★ 1.9k • written 4.2 years ago by ▴ 290
0
votes
3
replies
1.1k
views
monozygotic twins ped file specification
twin ped pedigree GATK
4.5 years ago by cocchi.e89 ▴ 290
0
votes
1
reply
1.1k
views
Comment: C: monozygotic twins ped file specification
4.5 years ago by cocchi.e89 ▴ 290
0
votes
1
reply
1.2k
views
cwl GATK GenotypeGVCFs error in linux due to quotes in filenames
gatk cwl GenotypeGVCFs
updated 3.9 years ago by ★ 1.9k • written 4.5 years ago by ▴ 290
1
vote
3
replies
1.4k
views
covid-19 publicly available data
covid clinical data
updated 4.6 years ago by 35k • written 5.2 years ago by ▴ 290
0
votes
0
replies
1.7k
views
GATK somatic CNV results
gatk cnv somatic
4.7 years ago by cocchi.e89 ▴ 290
0
votes
1
reply
1.9k
views
VEP - gnomAD v3 (hg38) annotation AF
VEP hg38 gnomAD annotation
updated 4.7 years ago by 20 • written 4.7 years ago by ▴ 290
0
votes
2
replies
2.4k
views
panel of normal files
gatk mutect2 panel-of-normal hg38 hg19
updated 4.7 years ago by • 0 • written 5.1 years ago by ▴ 290
1
vote
1
reply
1.2k
views
CNV .vcf retrieve involved genes
cnv vcf gatk genes
4.8 years ago by cocchi.e89 ▴ 290
1
vote
1
reply
1.6k
views
convert GATK germline CNV .vcf output to .seg/.cns format to plot
gatk cnv vcf seg cns
updated 4.8 years ago by ▴ 370 • written 4.8 years ago by ▴ 290
0
votes
1
reply
14k
views
Comment: C: all coding regions .bed file hg38 Whole Genome Sequencing
4.8 years ago by cocchi.e89 ▴ 290
0
votes
1
reply
14k
views
Comment: C: all coding regions .bed file hg38 Whole Genome Sequencing
4.8 years ago by cocchi.e89 ▴ 290
12
votes
13
replies
14k
views
7 follow
all coding regions .bed file hg38 Whole Genome Sequencing
wgs coding bed
updated 20 months ago by 45k • written 4.8 years ago by ▴ 290
1
vote
2
replies
1.3k
views
comparison of variants between WGS samples
wgs human gatk differences variants
updated 4.8 years ago by ★ 5.0k • written 4.8 years ago by ▴ 290
1
vote
1
reply
2.0k
views
GATK CNV germline plot vcf results
gatk cnv germline plot vcf
4.8 years ago by cocchi.e89 ▴ 290
0
votes
0
replies
1.5k
views
Comment: C: Error in GATK germline CNV caller
4.8 years ago by cocchi.e89 ▴ 290
1
vote
2
replies
1.5k
views
Error in GATK germline CNV caller
gatk cnv germline
4.8 years ago by cocchi.e89 ▴ 290
2
votes
1
reply
1.2k
views
cwl: pass array of elements with repeated input flags
cwl array gatk
4.8 years ago by cocchi.e89 ▴ 290
1
vote
0
replies
1.9k
views
GATK Mutect2 tumor-segmentation table
gatk mutect2 somatic
4.9 years ago by cocchi.e89 ▴ 290
1
vote
2
replies
2.1k
views
WGS hg19/hg38 Panel-of-Normals (GATK SV-CNV)
gatk PoN Panel-of-Normals CNV SV
4.9 years ago by cocchi.e89 ▴ 290
0
votes
0
replies
8.0k
views
Comment: C: GATK Mutect2 Panel-Of-Normals generation
4.9 years ago by cocchi.e89 ▴ 290
0
votes
0
replies
8.0k
views
Comment: C: GATK Mutect2 Panel-Of-Normals generation
5.0 years ago by cocchi.e89 ▴ 290
3
votes
1
reply
1.3k
views
gnomAD Structural Variants pipeline usage
gnomad sv talkowski-lab pipeline
5.0 years ago by cocchi.e89 ▴ 290
2
votes
0
replies
1.3k
views
Answer: A: gnomAD Structural Variants pipeline usage
5.0 years ago by cocchi.e89 ▴ 290
129 results • Page 1 of 3
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