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What happens to the genotype field in a g.vcf after CombineGVCFs
GT GATK CombineGVCFs genotype
updated 2.9 years ago by ▴ 20 • written 3.0 years ago by ▴ 310
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1
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1.9k
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Comment: Comment: Ambiguous SNPs
2.9 years ago by nhaus ▴ 310
2
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3
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1.9k
views
Ambiguous SNPs
SNPs
updated 2.9 years ago by 23k • written 2.9 years ago by ▴ 310
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0
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427
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Illumina Omni2.5 genotyping get actual genotypes.
genotyping omni illumina
2.9 years ago by nhaus ▴ 310
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0
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1.3k
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Comment: Comment: SHAPEIT v4 modify keep QUAL FORMAT and INFO field
3.0 years ago by nhaus ▴ 310
2
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5
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1.3k
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SHAPEIT v4 modify keep QUAL FORMAT and INFO field
shapeit phasing haplotype
3.0 years ago by nhaus ▴ 310
0
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1
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3.3k
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Comment: Comment: VEP is very slow. Fork doesnt seem to work
3.0 years ago by nhaus ▴ 310
1
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3
replies
1.4k
views
GATK ApplyVQSR filtering doesnt work
gatk variant calling germline
3.0 years ago by nhaus ▴ 310
1
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0
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1.4k
views
Answer: Answer: GATK ApplyVQSR filtering doesnt work
3.0 years ago by nhaus ▴ 310
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0
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1.4k
views
Comment: Comment: GATK ApplyVQSR filtering doesnt work
3.0 years ago by nhaus ▴ 310
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0
replies
1.9k
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Comment: Comment: Liftover vcf file from hs37d5 assembly to b37 assembly
3.0 years ago by nhaus ▴ 310
0
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1
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1.9k
views
Comment: Comment: Liftover vcf file from hs37d5 assembly to b37 assembly
3.0 years ago by nhaus ▴ 310
1
vote
5
replies
1.9k
views
Liftover vcf file from hs37d5 assembly to b37 assembly
vcf liftover assembly
updated 2.7 years ago by ▴ 90 • written 3.0 years ago by ▴ 310
1
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0
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1.2k
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Comment: Comment: High confident germline SNP and INDELS for VQSR for reference genome GRCh37
3.0 years ago by nhaus ▴ 310
5
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2
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1.2k
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High confident germline SNP and INDELS for VQSR for reference genome GRCh37
INDEL SNP 1000g GRCh37
3.0 years ago by nhaus ▴ 310
0
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1
reply
663
views
Predicting Drug responds from somatic mutations
prediction somatic responds drug
updated 3.0 years ago by ▴ 570 • written 3.0 years ago by ▴ 310
1
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4
replies
1.5k
views
Create Mutational signature plot from vcf file.
R python mutational
3.0 years ago by nhaus ▴ 310
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0
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1.5k
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Answer: Answer: Create Mutational signature plot from vcf file.
3.0 years ago by nhaus ▴ 310
0
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0
replies
1.5k
views
Comment: Comment: Create Mutational signature plot from vcf file.
3.0 years ago by nhaus ▴ 310
0
votes
1
reply
783
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Comment: C: conceptual question about paired end sequencing
3.1 years ago by nhaus ▴ 310
3
votes
5
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783
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conceptual question about paired end sequencing
sequencing illumina
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 310
4
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5
replies
3.3k
views
VEP is very slow. Fork doesnt seem to work
vep annotation
3.0 years ago by nhaus ▴ 310
0
votes
1
reply
812
views
Experience with BaseRecalibratorSpark and ApplyBQSRSpark
gatk somatic mutations snp
updated 3.2 years ago by 6.4k • written 3.2 years ago by ▴ 310
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0
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875
views
Panel of normals for Mutect2 GRCh37
gatk broad mutect2
3.2 years ago by nhaus ▴ 310
1
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5
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879
views
biomaRt external_gene_name same entry multiple times when mapping to homolog mouse gene
ensembl mapping homology
3.2 years ago by nhaus ▴ 310
0
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0
replies
879
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Comment: C: biomaRt external_gene_name same entry multiple times when mapping to homolog mou
3.2 years ago by nhaus ▴ 310
0
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0
replies
423
views
chi-square test to identify significantly mutated genes
genome sequencing
3.3 years ago by nhaus ▴ 310
0
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0
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1.3k
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Comment: C: Duplicated genes in overrepresentation analysis (ORA)
3.3 years ago by nhaus ▴ 310
0
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1
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1.3k
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Comment: C: Duplicated genes in overrepresentation analysis (ORA)
3.3 years ago by nhaus ▴ 310
0
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4
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1.3k
views
Duplicated genes in overrepresentation analysis (ORA)
ORA GSEA
updated 3.3 years ago by ▴ 200 • written 3.3 years ago by ▴ 310
0
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0
replies
443
views
Proper way of comparing list of mutated genes
gene GSEA
3.3 years ago by nhaus ▴ 310
0
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1
reply
992
views
Comment: C: Count, LT, PH, PT Column in Functional Annotation Chart of DAVID
3.3 years ago by nhaus ▴ 310
3
votes
3
replies
992
views
Count, LT, PH, PT Column in Functional Annotation Chart of DAVID
DAVID GSEA
updated 3.3 years ago by 10k • written 3.3 years ago by ▴ 310
0
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0
replies
641
views
versioned transcripts with SnpEff GRCh37
SnpEff annotation
3.4 years ago by nhaus ▴ 310
0
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0
replies
872
views
Comment: C: GT 0/0 in VCF file
3.4 years ago by nhaus ▴ 310
2
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2
replies
872
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GT 0/0 in VCF file
genome
3.4 years ago by nhaus ▴ 310
1
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0
replies
25k
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Answer: A: Extract Base Based On Position From Bam File
3.5 years ago by nhaus ▴ 310
0
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0
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632
views
Comment: C: Using StringTie with CAGE-seq data
3.7 years ago by nhaus ▴ 310
0
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3
replies
632
views
Using StringTie with CAGE-seq data
StringTie
3.7 years ago by nhaus ▴ 310
0
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5
replies
2.6k
views
Merging BAM vs concatenate FASTQ
sequencing genome
3.7 years ago by nhaus ▴ 310
0
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1
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2.9k
views
Comment: C: Questions about reference genome and alignment
3.7 years ago by nhaus ▴ 310
0
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1
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2.9k
views
Comment: C: Questions about reference genome and alignment
3.7 years ago by nhaus ▴ 310
4
votes
9
replies
2.9k
views
Questions about reference genome and alignment
genome alignment assembly
updated 3.7 years ago by 13k • written 3.7 years ago by ▴ 310
1
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1
reply
916
views
How to download BAM file from VM
bam VM
updated 13 months ago by 43k • written 3.8 years ago by ▴ 310
0
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0
replies
634
views
Find out genome version given fasta file
genome assembly
3.9 years ago by nhaus ▴ 310
0
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0
replies
2.3k
views
Comment: C: Getting the db SNP VCF file for GRCh38.p13
3.9 years ago by nhaus ▴ 310
0
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2
replies
2.3k
views
Getting the db SNP VCF file for GRCh38.p13
SNP dbSNP VCF
updated 3.9 years ago by 11k • written 3.9 years ago by ▴ 310
0
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1
reply
714
views
Questions regarding whole exome sequencing
WES sequencing
updated 3.9 years ago by 87k • written 3.9 years ago by ▴ 310
0
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0
replies
998
views
Comment: C: How to performe differential gene expression analysis for a single patient
4.0 years ago by nhaus ▴ 310
0
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1
reply
998
views
Comment: C: How to performe differential gene expression analysis for a single patient
4.0 years ago by nhaus ▴ 310
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