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SnpSift to annotate vcf with multiple databases
annotate vcf SnpSift
updated 14 months ago by ▴ 60 • written 2.4 years ago by ▴ 60
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457
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Comment: Comment: liftover bed not matching panel gene names
21 months ago by whb ▴ 60
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1
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457
views
liftover bed not matching panel gene names
liftover vcf bed bedtools
21 months ago by whb ▴ 60
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0
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646
views
Using snpsift to annotate vcf with dbsnp and Clinvar
snpsift
2.0 years ago by whb ▴ 60
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0
replies
405
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Real variant - Minimum allele frequency and alt count?
alt somatic af vcf
2.0 years ago by whb ▴ 60
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0
replies
544
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Comment: Comment: Mutations in contiguous sites within a sample
2.0 years ago by whb ▴ 60
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2
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544
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Mutations in contiguous sites within a sample
snp vcf
2.0 years ago by whb ▴ 60
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0
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937
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Comment: Comment: Determine strand info of somatic mutations
2.1 years ago by whb ▴ 60
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1
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937
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Comment: Comment: Determine strand info of somatic mutations
2.1 years ago by whb ▴ 60
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5
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937
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Determine strand info of somatic mutations
strand DNA
updated 2.1 years ago by 21k • written 2.1 years ago by ▴ 60
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0
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1.1k
views
Comment: Comment: lofreq empty output?
2.3 years ago by whb ▴ 60
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0
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426
views
dbSNP specific to C57BL6J
c57bl6j dbsnp
updated 2.4 years ago by 82k • written 2.4 years ago by ▴ 60
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0
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448
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detect and combine indels into one line like Mutect2 format
indels snvs vcf
2.4 years ago by whb ▴ 60
1
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5
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1.5k
views
bed intersect to get gene names from bed
bedtools intersect
updated 2.5 years ago by 35k • written 2.5 years ago by ▴ 60
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0
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1.5k
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Comment: Comment: bed intersect to get gene names from bed
2.5 years ago by whb ▴ 60
0
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1
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1.5k
views
Comment: Comment: bed intersect to get gene names from bed
2.5 years ago by whb ▴ 60
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0
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460
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filter Refseq file with bed? to produce coverage per gene
coverage bed refseq
2.5 years ago by whb ▴ 60
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1
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1.5k
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Comment: Comment: DepthOfCoverage Error: no suitable codec found
2.5 years ago by whb ▴ 60
1
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3
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1.5k
views
DepthOfCoverage Error: no suitable codec found
Coverage DepthOfCoverage Depth
updated 2.5 years ago by 161k • written 2.5 years ago by ▴ 60
4
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6
replies
1.4k
views
A bash question
bash
updated 2.6 years ago by 142k • written 2.6 years ago by ▴ 60
0
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1
reply
663
views
What determine if a panel can be used for copy number analysis?
panel copy number targeted
updated 3.0 years ago by ★ 2.9k • written 3.0 years ago by ▴ 60
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1
reply
738
views
driver genes per sample or per group?
driver genes
updated 14 months ago by ▴ 860 • written 3.1 years ago by ▴ 60
2
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2
replies
867
views
Convert protein name to letter e.g. p.Arg135Trp to p.R135W
aminoacid
updated 3.1 years ago by 21k • written 3.1 years ago by ▴ 60
1
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2
replies
692
views
Gene expression and chromatin state
DNA expression chromatin
3.2 years ago by whb ▴ 60
0
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0
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437
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How many variant caller is needed for somatic mutations?
SNP variant caller
3.2 years ago by whb ▴ 60
1
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0
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652
views
Tumour mutation burden vs mutant cells ratio vs Variant allele fraction
vaf maf tmb
3.2 years ago by whb ▴ 60
0
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0
replies
820
views
Filtering vcf with dbSNP
dbSNP filter bcftools
updated 3.2 years ago by 20 • written 3.3 years ago by ▴ 60
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0
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548
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bcftools isec: tandem mutations
bcftools isesc
3.3 years ago by whb ▴ 60
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0
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5.3k
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Comment: C: bcftools filter or bcftools isec to EXCLUDE dbSNP snps
3.3 years ago by whb ▴ 60
0
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1
reply
5.3k
views
Comment: C: bcftools filter or bcftools isec to EXCLUDE dbSNP snps
3.3 years ago by whb ▴ 60
0
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0
replies
550
views
Refseq file 0 coding length
gatk DepthOfCoverage
updated 3.3 years ago by 15k • written 3.3 years ago by ▴ 60
1
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5
replies
2.9k
views
Which adapters to use for trimming?
trimming adapters trimmomatic
updated 3.3 years ago by 20 • written 3.4 years ago by ▴ 60
0
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1
reply
903
views
Comment: C: NCBI build=37 in MAF despite using GRCm38 all along the variant calling workflow
3.4 years ago by whb ▴ 60
0
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3
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903
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NCBI build=37 in MAF despite using GRCm38 all along the variant calling workflow
MAF genome reference GRCm38 NCBI build
3.4 years ago by whb ▴ 60
0
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0
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847
views
Different dbSNP files input yield different variants?
SNP gatk dbSNP mutect2
3.4 years ago by whb ▴ 60
0
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1
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908
views
Comment: C: Snpefftomaf error: Changing the format column in vcf file
3.4 years ago by whb ▴ 60
0
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3
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908
views
Snpefftomaf error: Changing the format column in vcf file
vcf maf snpeff snpefftomaf
3.4 years ago by whb ▴ 60
0
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0
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7.9k
views
Comment: C: BWA error: no ID within the read group line
3.4 years ago by whb ▴ 60
0
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2
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7.9k
views
Comment: C: BWA error: no ID within the read group line
3.4 years ago by whb ▴ 60
4
votes
12
replies
7.9k
views
6 follow
BWA error: no ID within the read group line
bwa readgroups RG parallel
updated 3 months ago by ▴ 10 • written 3.4 years ago by ▴ 60
0
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1
reply
679
views
Difference between dbSNP vcfs
dbSNP SNP vcf
updated 3.4 years ago by ▴ 10 • written 3.4 years ago by ▴ 60
0
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1
reply
1.1k
views
samtools idxstats showing accession number and genomic scaffold
samtools idxstats bams
updated 3.4 years ago by 161k • written 3.4 years ago by ▴ 60
0
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0
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1.8k
views
Known-variant and AF-only files of GATK Mutect2 on Mouse DNA sequencing data
gatk mutect mouse SNP baserecalibrator
3.4 years ago by whb ▴ 60
5
votes
2
replies
2.9k
views
FASTQC after trimming: how do I know if it is good enough to proceed to alignment?
FASTQC Trimming per base sequence content
3.4 years ago by whb ▴ 60
0
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0
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7.9k
views
Comment: C: BWA error: no ID within the read group line
3.4 years ago by whb ▴ 60
0
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1
reply
7.9k
views
Comment: C: BWA error: no ID within the read group line
3.4 years ago by whb ▴ 60
0
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0
replies
1.4k
views
Comment: C: Tools for DNA sequencing saturation analysis
3.4 years ago by whb ▴ 60
0
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1
reply
1.4k
views
Comment: C: Tools for DNA sequencing saturation analysis
3.4 years ago by whb ▴ 60
1
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4
replies
1.4k
views
Tools for DNA sequencing saturation analysis
snp dna saturation analysis coverage
3.4 years ago by whb ▴ 60
0
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2
replies
744
views
Using Parallel GNU
parallel unix trimming
updated 3.4 years ago by 43k • written 3.4 years ago by ▴ 60
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