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636
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SnpSift to annotate vcf with multiple databases
annotate vcf SnpSift
updated 6 months ago by ▴ 60 • written 21 months ago by ▴ 50
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0
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330
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Comment: Comment: liftover bed not matching panel gene names
13 months ago by whb ▴ 50
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1
reply
330
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liftover bed not matching panel gene names
liftover vcf bed bedtools
13 months ago by whb ▴ 50
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0
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521
views
Using snpsift to annotate vcf with dbsnp and Clinvar
snpsift
16 months ago by whb ▴ 50
0
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0
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307
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Real variant - Minimum allele frequency and alt count?
alt somatic af vcf
16 months ago by whb ▴ 50
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0
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395
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Comment: Comment: Mutations in contiguous sites within a sample
16 months ago by whb ▴ 50
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2
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395
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Mutations in contiguous sites within a sample
snp vcf
16 months ago by whb ▴ 50
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0
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670
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Comment: Comment: Determine strand info of somatic mutations
17 months ago by whb ▴ 50
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1
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670
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Comment: Comment: Determine strand info of somatic mutations
18 months ago by whb ▴ 50
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5
replies
670
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Determine strand info of somatic mutations
strand DNA
updated 17 months ago by 21k • written 18 months ago by ▴ 50
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0
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910
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Comment: Comment: lofreq empty output?
20 months ago by whb ▴ 50
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0
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325
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dbSNP specific to C57BL6J
c57bl6j dbsnp
updated 21 months ago by 76k • written 21 months ago by ▴ 50
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0
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342
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detect and combine indels into one line like Mutect2 format
indels snvs vcf
21 months ago by whb ▴ 50
1
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5
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1.2k
views
bed intersect to get gene names from bed
bedtools intersect
updated 22 months ago by 35k • written 22 months ago by ▴ 50
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0
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1.2k
views
Comment: Comment: bed intersect to get gene names from bed
22 months ago by whb ▴ 50
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1
reply
1.2k
views
Comment: Comment: bed intersect to get gene names from bed
22 months ago by whb ▴ 50
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0
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364
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filter Refseq file with bed? to produce coverage per gene
coverage bed refseq
22 months ago by whb ▴ 50
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1
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1.2k
views
Comment: Comment: DepthOfCoverage Error: no suitable codec found
22 months ago by whb ▴ 50
1
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3
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1.2k
views
DepthOfCoverage Error: no suitable codec found
Coverage DepthOfCoverage Depth
updated 22 months ago by 157k • written 22 months ago by ▴ 50
4
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6
replies
1.2k
views
A bash question
bash
updated 23 months ago by 134k • written 23 months ago by ▴ 50
0
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1
reply
543
views
What determine if a panel can be used for copy number analysis?
panel copy number targeted
updated 2.4 years ago by ★ 2.9k • written 2.4 years ago by ▴ 50
0
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1
reply
564
views
driver genes per sample or per group?
driver genes
updated 6 months ago by ▴ 750 • written 2.5 years ago by ▴ 50
2
votes
2
replies
740
views
Convert protein name to letter e.g. p.Arg135Trp to p.R135W
aminoacid
updated 2.5 years ago by 21k • written 2.5 years ago by ▴ 50
1
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2
replies
547
views
Gene expression and chromatin state
DNA expression chromatin
2.6 years ago by whb ▴ 50
0
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0
replies
367
views
How many variant caller is needed for somatic mutations?
SNP variant caller
2.6 years ago by whb ▴ 50
1
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0
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538
views
Tumour mutation burden vs mutant cells ratio vs Variant allele fraction
vaf maf tmb
2.6 years ago by whb ▴ 50
0
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0
replies
704
views
Filtering vcf with dbSNP
dbSNP filter bcftools
updated 2.6 years ago by 20 • written 2.6 years ago by ▴ 50
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0
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468
views
bcftools isec: tandem mutations
bcftools isesc
2.6 years ago by whb ▴ 50
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0
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4.9k
views
Comment: C: bcftools filter or bcftools isec to EXCLUDE dbSNP snps
2.6 years ago by whb ▴ 50
0
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1
reply
4.9k
views
Comment: C: bcftools filter or bcftools isec to EXCLUDE dbSNP snps
2.6 years ago by whb ▴ 50
0
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0
replies
483
views
Refseq file 0 coding length
gatk DepthOfCoverage
updated 2.6 years ago by 14k • written 2.6 years ago by ▴ 50
1
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5
replies
2.4k
views
Which adapters to use for trimming?
trimming adapters trimmomatic
updated 2.7 years ago by 20 • written 2.8 years ago by ▴ 50
0
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1
reply
736
views
Comment: C: NCBI build=37 in MAF despite using GRCm38 all along the variant calling workflow
2.7 years ago by whb ▴ 50
0
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3
replies
736
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NCBI build=37 in MAF despite using GRCm38 all along the variant calling workflow
MAF genome reference GRCm38 NCBI build
2.7 years ago by whb ▴ 50
0
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0
replies
725
views
Different dbSNP files input yield different variants?
SNP gatk dbSNP mutect2
2.7 years ago by whb ▴ 50
0
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1
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753
views
Comment: C: Snpefftomaf error: Changing the format column in vcf file
2.7 years ago by whb ▴ 50
0
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3
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753
views
Snpefftomaf error: Changing the format column in vcf file
vcf maf snpeff snpefftomaf
2.7 years ago by whb ▴ 50
0
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0
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6.4k
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Comment: C: BWA error: no ID within the read group line
2.7 years ago by whb ▴ 50
0
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2
replies
6.4k
views
Comment: C: BWA error: no ID within the read group line
2.7 years ago by whb ▴ 50
3
votes
11
replies
6.4k
views
BWA error: no ID within the read group line
bwa readgroups RG parallel
updated 19 months ago by 40k • written 2.8 years ago by ▴ 50
0
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1
reply
567
views
Difference between dbSNP vcfs
dbSNP SNP vcf
updated 2.7 years ago by ▴ 10 • written 2.7 years ago by ▴ 50
0
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1
reply
926
views
samtools idxstats showing accession number and genomic scaffold
samtools idxstats bams
updated 2.7 years ago by 157k • written 2.7 years ago by ▴ 50
0
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0
replies
1.5k
views
Known-variant and AF-only files of GATK Mutect2 on Mouse DNA sequencing data
gatk mutect mouse SNP baserecalibrator
2.7 years ago by whb ▴ 50
3
votes
2
replies
2.3k
views
FASTQC after trimming: how do I know if it is good enough to proceed to alignment?
FASTQC Trimming per base sequence content
2.7 years ago by whb ▴ 50
0
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0
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6.4k
views
Comment: C: BWA error: no ID within the read group line
2.8 years ago by whb ▴ 50
0
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1
reply
6.4k
views
Comment: C: BWA error: no ID within the read group line
2.8 years ago by whb ▴ 50
0
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0
replies
1.2k
views
Comment: C: Tools for DNA sequencing saturation analysis
2.8 years ago by whb ▴ 50
0
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1
reply
1.2k
views
Comment: C: Tools for DNA sequencing saturation analysis
2.8 years ago by whb ▴ 50
1
vote
4
replies
1.2k
views
Tools for DNA sequencing saturation analysis
snp dna saturation analysis coverage
2.8 years ago by whb ▴ 50
0
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2
replies
603
views
Using Parallel GNU
parallel unix trimming
updated 2.8 years ago by 40k • written 2.8 years ago by ▴ 50
51 results • Page 1 of 2
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