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971
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SnpSift to annotate vcf with multiple databases
annotate vcf SnpSift
updated 20 months ago by ▴ 80 • written 2.9 years ago by ▴ 60
0
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0
replies
550
views
Comment: Comment: liftover bed not matching panel gene names
2.3 years ago by whb ▴ 60
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1
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550
views
liftover bed not matching panel gene names
liftover vcf bed bedtools
2.3 years ago by whb ▴ 60
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0
replies
735
views
Using snpsift to annotate vcf with dbsnp and Clinvar
snpsift
2.5 years ago by whb ▴ 60
0
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0
replies
473
views
Real variant - Minimum allele frequency and alt count?
alt somatic af vcf
2.5 years ago by whb ▴ 60
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0
replies
647
views
Comment: Comment: Mutations in contiguous sites within a sample
2.5 years ago by whb ▴ 60
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2
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647
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Mutations in contiguous sites within a sample
snp vcf
2.5 years ago by whb ▴ 60
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0
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1.2k
views
Comment: Comment: Determine strand info of somatic mutations
2.6 years ago by whb ▴ 60
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1
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1.2k
views
Comment: Comment: Determine strand info of somatic mutations
2.6 years ago by whb ▴ 60
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5
replies
1.2k
views
Determine strand info of somatic mutations
strand DNA
updated 2.6 years ago by 21k • written 2.6 years ago by ▴ 60
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0
replies
1.2k
views
Comment: Comment: lofreq empty output?
2.8 years ago by whb ▴ 60
0
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0
replies
488
views
dbSNP specific to C57BL6J
c57bl6j dbsnp
updated 2.9 years ago by 85k • written 2.9 years ago by ▴ 60
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0
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504
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detect and combine indels into one line like Mutect2 format
indels snvs vcf
2.9 years ago by whb ▴ 60
1
vote
5
replies
1.7k
views
bed intersect to get gene names from bed
bedtools intersect
updated 3.0 years ago by 35k • written 3.0 years ago by ▴ 60
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0
replies
1.7k
views
Comment: Comment: bed intersect to get gene names from bed
3.0 years ago by whb ▴ 60
0
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1
reply
1.7k
views
Comment: Comment: bed intersect to get gene names from bed
3.0 years ago by whb ▴ 60
0
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0
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505
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filter Refseq file with bed? to produce coverage per gene
coverage bed refseq
3.0 years ago by whb ▴ 60
0
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1
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1.6k
views
Comment: Comment: DepthOfCoverage Error: no suitable codec found
3.0 years ago by whb ▴ 60
1
vote
3
replies
1.6k
views
DepthOfCoverage Error: no suitable codec found
Coverage DepthOfCoverage Depth
updated 3.0 years ago by 164k • written 3.0 years ago by ▴ 60
4
votes
6
replies
1.5k
views
A bash question
bash
updated 3.1 years ago by 147k • written 3.1 years ago by ▴ 60
0
votes
1
reply
736
views
What determine if a panel can be used for copy number analysis?
panel copy number targeted
updated 3.5 years ago by ★ 2.9k • written 3.5 years ago by ▴ 60
0
votes
1
reply
835
views
driver genes per sample or per group?
driver genes
updated 21 months ago by ▴ 920 • written 3.6 years ago by ▴ 60
2
votes
2
replies
953
views
Convert protein name to letter e.g. p.Arg135Trp to p.R135W
aminoacid
updated 3.6 years ago by 21k • written 3.6 years ago by ▴ 60
1
vote
2
replies
759
views
Gene expression and chromatin state
DNA expression chromatin
3.7 years ago by whb ▴ 60
0
votes
0
replies
492
views
How many variant caller is needed for somatic mutations?
SNP variant caller
3.7 years ago by whb ▴ 60
1
vote
0
replies
728
views
Tumour mutation burden vs mutant cells ratio vs Variant allele fraction
vaf maf tmb
3.7 years ago by whb ▴ 60
0
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0
replies
874
views
Filtering vcf with dbSNP
dbSNP filter bcftools
updated 3.7 years ago by 20 • written 3.8 years ago by ▴ 60
0
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0
replies
600
views
bcftools isec: tandem mutations
bcftools isesc
3.8 years ago by whb ▴ 60
0
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0
replies
5.6k
views
Comment: C: bcftools filter or bcftools isec to EXCLUDE dbSNP snps
3.8 years ago by whb ▴ 60
0
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1
reply
5.6k
views
Comment: C: bcftools filter or bcftools isec to EXCLUDE dbSNP snps
3.8 years ago by whb ▴ 60
0
votes
0
replies
603
views
Refseq file 0 coding length
gatk DepthOfCoverage
updated 3.8 years ago by 15k • written 3.8 years ago by ▴ 60
1
vote
5
replies
3.3k
views
Which adapters to use for trimming?
trimming adapters trimmomatic
updated 3.8 years ago by 20 • written 3.9 years ago by ▴ 60
0
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1
reply
1.0k
views
Comment: C: NCBI build=37 in MAF despite using GRCm38 all along the variant calling workflow
3.9 years ago by whb ▴ 60
0
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3
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1.0k
views
NCBI build=37 in MAF despite using GRCm38 all along the variant calling workflow
MAF genome reference GRCm38 NCBI build
3.9 years ago by whb ▴ 60
0
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0
replies
948
views
Different dbSNP files input yield different variants?
SNP gatk dbSNP mutect2
3.9 years ago by whb ▴ 60
0
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1
reply
1.0k
views
Comment: C: Snpefftomaf error: Changing the format column in vcf file
3.9 years ago by whb ▴ 60
0
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3
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1.0k
views
Snpefftomaf error: Changing the format column in vcf file
vcf maf snpeff snpefftomaf
3.9 years ago by whb ▴ 60
0
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0
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8.7k
views
Comment: C: BWA error: no ID within the read group line
3.9 years ago by whb ▴ 60
0
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2
replies
8.7k
views
Comment: C: BWA error: no ID within the read group line
3.9 years ago by whb ▴ 60
4
votes
12
replies
8.7k
views
6 follow
BWA error: no ID within the read group line
bwa readgroups RG parallel
updated 9 months ago by ▴ 10 • written 3.9 years ago by ▴ 60
0
votes
1
reply
750
views
Difference between dbSNP vcfs
dbSNP SNP vcf
updated 3.9 years ago by ▴ 10 • written 3.9 years ago by ▴ 60
0
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1
reply
1.2k
views
samtools idxstats showing accession number and genomic scaffold
samtools idxstats bams
updated 3.9 years ago by 164k • written 3.9 years ago by ▴ 60
0
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0
replies
2.1k
views
Known-variant and AF-only files of GATK Mutect2 on Mouse DNA sequencing data
gatk mutect mouse SNP baserecalibrator
3.9 years ago by whb ▴ 60
5
votes
2
replies
3.3k
views
FASTQC after trimming: how do I know if it is good enough to proceed to alignment?
FASTQC Trimming per base sequence content
3.9 years ago by whb ▴ 60
0
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0
replies
8.7k
views
Comment: C: BWA error: no ID within the read group line
3.9 years ago by whb ▴ 60
0
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1
reply
8.7k
views
Comment: C: BWA error: no ID within the read group line
3.9 years ago by whb ▴ 60
0
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0
replies
1.6k
views
Comment: C: Tools for DNA sequencing saturation analysis
3.9 years ago by whb ▴ 60
0
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1
reply
1.6k
views
Comment: C: Tools for DNA sequencing saturation analysis
4.0 years ago by whb ▴ 60
1
vote
4
replies
1.6k
views
Tools for DNA sequencing saturation analysis
snp dna saturation analysis coverage
4.0 years ago by whb ▴ 60
0
votes
2
replies
853
views
Using Parallel GNU
parallel unix trimming
updated 4.0 years ago by 44k • written 4.0 years ago by ▴ 60
51 results • Page 1 of 2
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