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2
votes
4
replies
869
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Why are there nucleotides in the reference genome which are also minor alleles in the 1000 genomes project
reference genotype minor allele
updated 2.9 years ago by 47k • written 2.9 years ago by ▴ 360
1
vote
1
reply
1.1k
views
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 ▴ 360
0
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1
reply
1.9k
views
Comment: Comment: Ambiguous SNPs
2.9 years ago by nhaus ▴ 360
2
votes
3
replies
1.9k
views
Ambiguous SNPs
SNPs
updated 2.9 years ago by 23k • written 2.9 years ago by ▴ 360
0
votes
0
replies
431
views
Illumina Omni2.5 genotyping get actual genotypes.
genotyping omni illumina
3.0 years ago by nhaus ▴ 360
0
votes
0
replies
1.3k
views
Comment: Comment: SHAPEIT v4 modify keep QUAL FORMAT and INFO field
3.0 years ago by nhaus ▴ 360
2
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5
replies
1.3k
views
SHAPEIT v4 modify keep QUAL FORMAT and INFO field
shapeit phasing haplotype
3.0 years ago by nhaus ▴ 360
0
votes
1
reply
3.3k
views
Comment: Comment: VEP is very slow. Fork doesnt seem to work
3.0 years ago by nhaus ▴ 360
1
vote
3
replies
1.4k
views
GATK ApplyVQSR filtering doesnt work
gatk variant calling germline
3.0 years ago by nhaus ▴ 360
1
vote
0
replies
1.4k
views
Answer: Answer: GATK ApplyVQSR filtering doesnt work
3.0 years ago by nhaus ▴ 360
0
votes
0
replies
1.4k
views
Comment: Comment: GATK ApplyVQSR filtering doesnt work
3.0 years ago by nhaus ▴ 360
0
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0
replies
1.9k
views
Comment: Comment: Liftover vcf file from hs37d5 assembly to b37 assembly
3.0 years ago by nhaus ▴ 360
0
votes
1
reply
1.9k
views
Comment: Comment: Liftover vcf file from hs37d5 assembly to b37 assembly
3.0 years ago by nhaus ▴ 360
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 ▴ 360
1
vote
0
replies
1.3k
views
Comment: Comment: High confident germline SNP and INDELS for VQSR for reference genome GRCh37
3.0 years ago by nhaus ▴ 360
5
votes
2
replies
1.3k
views
High confident germline SNP and INDELS for VQSR for reference genome GRCh37
INDEL SNP 1000g GRCh37
3.0 years ago by nhaus ▴ 360
0
votes
1
reply
672
views
Predicting Drug responds from somatic mutations
prediction somatic responds drug
updated 3.0 years ago by ▴ 570 • written 3.0 years ago by ▴ 360
1
vote
4
replies
1.5k
views
Create Mutational signature plot from vcf file.
R python mutational
3.1 years ago by nhaus ▴ 360
0
votes
0
replies
1.5k
views
Answer: Answer: Create Mutational signature plot from vcf file.
3.1 years ago by nhaus ▴ 360
0
votes
0
replies
1.5k
views
Comment: Comment: Create Mutational signature plot from vcf file.
3.1 years ago by nhaus ▴ 360
0
votes
1
reply
790
views
Comment: C: conceptual question about paired end sequencing
3.2 years ago by nhaus ▴ 360
3
votes
5
replies
790
views
conceptual question about paired end sequencing
sequencing illumina
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 360
4
votes
5
replies
3.3k
views
VEP is very slow. Fork doesnt seem to work
vep annotation
3.0 years ago by nhaus ▴ 360
0
votes
1
reply
817
views
Experience with BaseRecalibratorSpark and ApplyBQSRSpark
gatk somatic mutations snp
updated 3.2 years ago by 6.4k • written 3.3 years ago by ▴ 360
0
votes
0
replies
880
views
Panel of normals for Mutect2 GRCh37
gatk broad mutect2
3.3 years ago by nhaus ▴ 360
1
vote
5
replies
892
views
biomaRt external_gene_name same entry multiple times when mapping to homolog mouse gene
ensembl mapping homology
3.3 years ago by nhaus ▴ 360
0
votes
0
replies
892
views
Comment: C: biomaRt external_gene_name same entry multiple times when mapping to homolog mou
3.3 years ago by nhaus ▴ 360
0
votes
0
replies
424
views
chi-square test to identify significantly mutated genes
genome sequencing
3.3 years ago by nhaus ▴ 360
0
votes
0
replies
1.3k
views
Comment: C: Duplicated genes in overrepresentation analysis (ORA)
3.3 years ago by nhaus ▴ 360
0
votes
1
reply
1.3k
views
Comment: C: Duplicated genes in overrepresentation analysis (ORA)
3.3 years ago by nhaus ▴ 360
0
votes
4
replies
1.3k
views
Duplicated genes in overrepresentation analysis (ORA)
ORA GSEA
updated 3.3 years ago by ▴ 200 • written 3.3 years ago by ▴ 360
0
votes
0
replies
445
views
Proper way of comparing list of mutated genes
gene GSEA
3.3 years ago by nhaus ▴ 360
0
votes
1
reply
1.0k
views
Comment: C: Count, LT, PH, PT Column in Functional Annotation Chart of DAVID
3.3 years ago by nhaus ▴ 360
3
votes
3
replies
1.0k
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 ▴ 360
0
votes
0
replies
642
views
versioned transcripts with SnpEff GRCh37
SnpEff annotation
3.4 years ago by nhaus ▴ 360
0
votes
0
replies
879
views
Comment: C: GT 0/0 in VCF file
3.4 years ago by nhaus ▴ 360
2
votes
2
replies
879
views
GT 0/0 in VCF file
genome
3.4 years ago by nhaus ▴ 360
1
vote
0
replies
25k
views
Answer: A: Extract Base Based On Position From Bam File
3.5 years ago by nhaus ▴ 360
0
votes
0
replies
635
views
Comment: C: Using StringTie with CAGE-seq data
3.7 years ago by nhaus ▴ 360
0
votes
3
replies
635
views
Using StringTie with CAGE-seq data
StringTie
3.7 years ago by nhaus ▴ 360
0
votes
5
replies
2.6k
views
Merging BAM vs concatenate FASTQ
sequencing genome
3.7 years ago by nhaus ▴ 360
0
votes
1
reply
2.9k
views
Comment: C: Questions about reference genome and alignment
3.8 years ago by nhaus ▴ 360
0
votes
1
reply
2.9k
views
Comment: C: Questions about reference genome and alignment
3.8 years ago by nhaus ▴ 360
4
votes
9
replies
2.9k
views
Questions about reference genome and alignment
genome alignment assembly
updated 3.8 years ago by 13k • written 3.8 years ago by ▴ 360
1
vote
1
reply
922
views
How to download BAM file from VM
bam VM
updated 14 months ago by 43k • written 3.9 years ago by ▴ 360
0
votes
0
replies
636
views
Find out genome version given fasta file
genome assembly
3.9 years ago by nhaus ▴ 360
0
votes
0
replies
2.3k
views
Comment: C: Getting the db SNP VCF file for GRCh38.p13
4.0 years ago by nhaus ▴ 360
0
votes
2
replies
2.3k
views
Getting the db SNP VCF file for GRCh38.p13
SNP dbSNP VCF
updated 4.0 years ago by 11k • written 4.0 years ago by ▴ 360
0
votes
1
reply
721
views
Questions regarding whole exome sequencing
WES sequencing
updated 4.0 years ago by 88k • written 4.0 years ago by ▴ 360
0
votes
0
replies
1.0k
views
Comment: C: How to performe differential gene expression analysis for a single patient
4.0 years ago by nhaus ▴ 360
107 results • Page 2 of 3
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