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1.1k
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SnpSift to annotate vcf with multiple databases
annotate vcf SnpSift
updated 2.0 years ago by ▴ 80 • written 3.3 years ago by ▴ 60
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0
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650
views
Comment: Comment: liftover bed not matching panel gene names
2.6 years ago by whb ▴ 60
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1
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650
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liftover bed not matching panel gene names
liftover vcf bed bedtools
2.6 years ago by whb ▴ 60
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0
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815
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Using snpsift to annotate vcf with dbsnp and Clinvar
snpsift
2.9 years ago by whb ▴ 60
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0
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554
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Real variant - Minimum allele frequency and alt count?
alt somatic af vcf
2.9 years ago by whb ▴ 60
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0
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779
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Comment: Comment: Mutations in contiguous sites within a sample
2.9 years ago by whb ▴ 60
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2
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779
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Mutations in contiguous sites within a sample
snp vcf
2.9 years ago by whb ▴ 60
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0
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1.4k
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Comment: Comment: Determine strand info of somatic mutations
2.9 years ago by whb ▴ 60
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1
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1.4k
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Comment: Comment: Determine strand info of somatic mutations
3.0 years ago by whb ▴ 60
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5
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1.4k
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Determine strand info of somatic mutations
strand DNA
updated 2.9 years ago by 21k • written 3.0 years ago by ▴ 60
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0
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1.3k
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Comment: Comment: lofreq empty output?
3.2 years ago by whb ▴ 60
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0
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561
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dbSNP specific to C57BL6J
c57bl6j dbsnp
updated 3.2 years ago by 87k • written 3.2 years ago by ▴ 60
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0
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566
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detect and combine indels into one line like Mutect2 format
indels snvs vcf
3.3 years ago by whb ▴ 60
1
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5
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2.0k
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bed intersect to get gene names from bed
bedtools intersect
updated 3.4 years ago by 36k • written 3.4 years ago by ▴ 60
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0
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2.0k
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Comment: Comment: bed intersect to get gene names from bed
3.4 years ago by whb ▴ 60
0
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1
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2.0k
views
Comment: Comment: bed intersect to get gene names from bed
3.4 years ago by whb ▴ 60
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0
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541
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filter Refseq file with bed? to produce coverage per gene
coverage bed refseq
3.4 years ago by whb ▴ 60
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1
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1.8k
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Comment: Comment: DepthOfCoverage Error: no suitable codec found
3.4 years ago by whb ▴ 60
1
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3
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1.8k
views
DepthOfCoverage Error: no suitable codec found
Coverage DepthOfCoverage Depth
updated 3.4 years ago by 165k • written 3.4 years ago by ▴ 60
4
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6
replies
1.7k
views
A bash question
bash
updated 3.4 years ago by 150k • written 3.4 years ago by ▴ 60
0
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1
reply
824
views
What determine if a panel can be used for copy number analysis?
panel copy number targeted
updated 3.9 years ago by ★ 3.0k • written 3.9 years ago by ▴ 60
0
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1
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903
views
driver genes per sample or per group?
driver genes
updated 2.1 years ago by ▴ 930 • written 4.0 years ago by ▴ 60
2
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2
replies
1.0k
views
Convert protein name to letter e.g. p.Arg135Trp to p.R135W
aminoacid
updated 4.0 years ago by 21k • written 4.0 years ago by ▴ 60
1
vote
2
replies
807
views
Gene expression and chromatin state
DNA expression chromatin
4.1 years ago by whb ▴ 60
0
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0
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531
views
How many variant caller is needed for somatic mutations?
SNP variant caller
4.1 years ago by whb ▴ 60
1
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0
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805
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Tumour mutation burden vs mutant cells ratio vs Variant allele fraction
vaf maf tmb
4.1 years ago by whb ▴ 60
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0
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924
views
Filtering vcf with dbSNP
dbSNP filter bcftools
updated 4.1 years ago by 20 • written 4.1 years ago by ▴ 60
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0
replies
640
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bcftools isec: tandem mutations
bcftools isesc
4.1 years ago by whb ▴ 60
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0
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5.9k
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Comment: C: bcftools filter or bcftools isec to EXCLUDE dbSNP snps
4.1 years ago by whb ▴ 60
0
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1
reply
5.9k
views
Comment: C: bcftools filter or bcftools isec to EXCLUDE dbSNP snps
4.1 years ago by whb ▴ 60
0
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0
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637
views
Refseq file 0 coding length
gatk DepthOfCoverage
updated 4.1 years ago by 15k • written 4.1 years ago by ▴ 60
1
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5
replies
3.6k
views
Which adapters to use for trimming?
trimming adapters trimmomatic
updated 4.2 years ago by 20 • written 4.3 years ago by ▴ 60
0
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1
reply
1.1k
views
Comment: C: NCBI build=37 in MAF despite using GRCm38 all along the variant calling workflow
4.2 years ago by whb ▴ 60
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3
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1.1k
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NCBI build=37 in MAF despite using GRCm38 all along the variant calling workflow
MAF genome reference GRCm38 NCBI build
4.2 years ago by whb ▴ 60
0
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0
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1.0k
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Different dbSNP files input yield different variants?
SNP gatk dbSNP mutect2
4.2 years ago by whb ▴ 60
0
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1
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1.1k
views
Comment: C: Snpefftomaf error: Changing the format column in vcf file
4.2 years ago by whb ▴ 60
0
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3
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1.1k
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Snpefftomaf error: Changing the format column in vcf file
vcf maf snpeff snpefftomaf
4.2 years ago by whb ▴ 60
0
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0
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9.2k
views
Comment: C: BWA error: no ID within the read group line
4.2 years ago by whb ▴ 60
0
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2
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9.2k
views
Comment: C: BWA error: no ID within the read group line
4.2 years ago by whb ▴ 60
4
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12
replies
9.2k
views
6 follow
BWA error: no ID within the read group line
bwa readgroups RG parallel
updated 13 months ago by ▴ 10 • written 4.3 years ago by ▴ 60
0
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1
reply
827
views
Difference between dbSNP vcfs
dbSNP SNP vcf
updated 4.2 years ago by ▴ 10 • written 4.2 years ago by ▴ 60
0
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1
reply
1.3k
views
samtools idxstats showing accession number and genomic scaffold
samtools idxstats bams
updated 4.2 years ago by 165k • written 4.2 years ago by ▴ 60
0
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0
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2.2k
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Known-variant and AF-only files of GATK Mutect2 on Mouse DNA sequencing data
gatk mutect mouse SNP baserecalibrator
4.2 years ago by whb ▴ 60
5
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2
replies
3.6k
views
FASTQC after trimming: how do I know if it is good enough to proceed to alignment?
FASTQC Trimming per base sequence content
4.2 years ago by whb ▴ 60
0
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0
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9.2k
views
Comment: C: BWA error: no ID within the read group line
4.3 years ago by whb ▴ 60
0
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1
reply
9.2k
views
Comment: C: BWA error: no ID within the read group line
4.3 years ago by whb ▴ 60
0
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0
replies
1.7k
views
Comment: C: Tools for DNA sequencing saturation analysis
4.3 years ago by whb ▴ 60
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1
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1.7k
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Comment: C: Tools for DNA sequencing saturation analysis
4.3 years ago by whb ▴ 60
1
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4
replies
1.7k
views
Tools for DNA sequencing saturation analysis
snp dna saturation analysis coverage
4.3 years ago by whb ▴ 60
0
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2
replies
969
views
Using Parallel GNU
parallel unix trimming
updated 4.3 years ago by 45k • written 4.3 years ago by ▴ 60
51 results • Page 1 of 2
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