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SnpSift to annotate vcf with multiple databases
annotate vcf SnpSift
updated 2.6 years ago by ▴ 80 • written 3.8 years ago by ▴ 60
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0
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797
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Comment: Comment: liftover bed not matching panel gene names
3.2 years ago by whb ▴ 60
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1
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797
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liftover bed not matching panel gene names
liftover vcf bed bedtools
3.2 years ago by whb ▴ 60
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0
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914
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Using snpsift to annotate vcf with dbsnp and Clinvar
snpsift
3.4 years ago by whb ▴ 60
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0
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651
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Real variant - Minimum allele frequency and alt count?
alt somatic af vcf
3.4 years ago by whb ▴ 60
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0
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1.1k
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Comment: Comment: Mutations in contiguous sites within a sample
3.4 years ago by whb ▴ 60
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2
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1.1k
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Mutations in contiguous sites within a sample
snp vcf
3.4 years ago by whb ▴ 60
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0
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1.7k
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Comment: Comment: Determine strand info of somatic mutations
3.5 years ago by whb ▴ 60
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1
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1.7k
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Comment: Comment: Determine strand info of somatic mutations
3.5 years ago by whb ▴ 60
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5
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1.7k
views
Determine strand info of somatic mutations
strand DNA
updated 3.5 years ago by 21k • written 3.5 years ago by ▴ 60
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0
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1.4k
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Comment: Comment: lofreq empty output?
3.7 years ago by whb ▴ 60
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0
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643
views
dbSNP specific to C57BL6J
c57bl6j dbsnp
updated 3.8 years ago by 89k • written 3.8 years ago by ▴ 60
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0
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656
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detect and combine indels into one line like Mutect2 format
indels snvs vcf
3.8 years ago by whb ▴ 60
1
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5
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2.3k
views
bed intersect to get gene names from bed
bedtools intersect
updated 3.9 years ago by 36k • written 3.9 years ago by ▴ 60
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0
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2.3k
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Comment: Comment: bed intersect to get gene names from bed
3.9 years ago by whb ▴ 60
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1
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2.3k
views
Comment: Comment: bed intersect to get gene names from bed
3.9 years ago by whb ▴ 60
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0
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627
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filter Refseq file with bed? to produce coverage per gene
coverage bed refseq
3.9 years ago by whb ▴ 60
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1
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2.0k
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Comment: Comment: DepthOfCoverage Error: no suitable codec found
3.9 years ago by whb ▴ 60
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3
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2.0k
views
DepthOfCoverage Error: no suitable codec found
Coverage DepthOfCoverage Depth
updated 3.9 years ago by 166k • written 3.9 years ago by ▴ 60
4
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6
replies
2.0k
views
A bash question
bash
updated 4.0 years ago by 154k • written 4.0 years ago by ▴ 60
0
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1
reply
955
views
What determine if a panel can be used for copy number analysis?
panel copy number targeted
updated 4.4 years ago by ★ 3.0k • written 4.4 years ago by ▴ 60
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1
reply
1.1k
views
driver genes per sample or per group?
driver genes
updated 2.6 years ago by ▴ 940 • written 4.5 years ago by ▴ 60
2
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2
replies
1.3k
views
Convert protein name to letter e.g. p.Arg135Trp to p.R135W
aminoacid
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 60
1
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2
replies
921
views
Gene expression and chromatin state
DNA expression chromatin
4.6 years ago by whb ▴ 60
0
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0
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606
views
How many variant caller is needed for somatic mutations?
SNP variant caller
4.6 years ago by whb ▴ 60
1
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0
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932
views
Tumour mutation burden vs mutant cells ratio vs Variant allele fraction
vaf maf tmb
4.6 years ago by whb ▴ 60
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0
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1.0k
views
Filtering vcf with dbSNP
dbSNP filter bcftools
updated 4.6 years ago by 20 • written 4.7 years ago by ▴ 60
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0
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735
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bcftools isec: tandem mutations
bcftools isesc
4.7 years ago by whb ▴ 60
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0
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6.4k
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Comment: C: bcftools filter or bcftools isec to EXCLUDE dbSNP snps
4.7 years ago by whb ▴ 60
0
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1
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6.4k
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Comment: C: bcftools filter or bcftools isec to EXCLUDE dbSNP snps
4.7 years ago by whb ▴ 60
0
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0
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729
views
Refseq file 0 coding length
gatk DepthOfCoverage
updated 4.7 years ago by 16k • written 4.7 years ago by ▴ 60
1
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5
replies
4.3k
views
Which adapters to use for trimming?
trimming adapters trimmomatic
updated 4.7 years ago by 20 • written 4.8 years ago by ▴ 60
0
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1
reply
1.3k
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Comment: C: NCBI build=37 in MAF despite using GRCm38 all along the variant calling workflow
4.8 years ago by whb ▴ 60
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3
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1.3k
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NCBI build=37 in MAF despite using GRCm38 all along the variant calling workflow
MAF genome reference GRCm38 NCBI build
4.8 years ago by whb ▴ 60
0
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0
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1.2k
views
Different dbSNP files input yield different variants?
SNP gatk dbSNP mutect2
4.8 years ago by whb ▴ 60
0
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1
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1.3k
views
Comment: C: Snpefftomaf error: Changing the format column in vcf file
4.8 years ago by whb ▴ 60
0
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3
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1.3k
views
Snpefftomaf error: Changing the format column in vcf file
vcf maf snpeff snpefftomaf
4.8 years ago by whb ▴ 60
0
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0
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10.0k
views
Comment: C: BWA error: no ID within the read group line
4.8 years ago by whb ▴ 60
0
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2
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10.0k
views
Comment: C: BWA error: no ID within the read group line
4.8 years ago by whb ▴ 60
4
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12
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10.0k
views
6 follow
BWA error: no ID within the read group line
bwa readgroups RG parallel
updated 20 months ago by ▴ 10 • written 4.8 years ago by ▴ 60
0
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1
reply
1.0k
views
Difference between dbSNP vcfs
dbSNP SNP vcf
updated 4.8 years ago by ▴ 10 • written 4.8 years ago by ▴ 60
0
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1
reply
1.5k
views
samtools idxstats showing accession number and genomic scaffold
samtools idxstats bams
updated 4.8 years ago by 166k • written 4.8 years ago by ▴ 60
0
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0
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2.5k
views
Known-variant and AF-only files of GATK Mutect2 on Mouse DNA sequencing data
gatk mutect mouse SNP baserecalibrator
4.8 years ago by whb ▴ 60
5
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2
replies
3.9k
views
FASTQC after trimming: how do I know if it is good enough to proceed to alignment?
FASTQC Trimming per base sequence content
4.8 years ago by whb ▴ 60
0
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0
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10.0k
views
Comment: C: BWA error: no ID within the read group line
4.8 years ago by whb ▴ 60
0
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1
reply
10.0k
views
Comment: C: BWA error: no ID within the read group line
4.8 years ago by whb ▴ 60
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0
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2.0k
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Comment: C: Tools for DNA sequencing saturation analysis
4.8 years ago by whb ▴ 60
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1
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2.0k
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Comment: C: Tools for DNA sequencing saturation analysis
4.8 years ago by whb ▴ 60
1
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4
replies
2.0k
views
Tools for DNA sequencing saturation analysis
snp dna saturation analysis coverage
4.8 years ago by whb ▴ 60
0
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2
replies
1.2k
views
Using Parallel GNU
parallel unix trimming
updated 4.8 years ago by 45k • written 4.8 years ago by ▴ 60
51 results • Page 1 of 2
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