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4
votes
5
replies
428
views
Should we cite sed / awk in papers?
sed awk
updated 24 days ago by 87k • written 24 days ago by ▴ 250
0
votes
3
replies
566
views
Germline variant - should it be seen in the somatic vcf?
vcf somatic
updated 6 months ago by 45k • written 6 months ago by ▴ 250
0
votes
0
replies
310
views
Advice on telling if two SNPs are on the same haplotype
ldpair halplotype co-occurance gnomad snp
12 months ago by amy__ ▴ 250
0
votes
13
replies
1.8k
views
Help with the new nomenclature of multi-nucleotide variants
bam igv multinucleotide
12 months ago by amy__ ▴ 250
2
votes
4
replies
1.2k
views
If the mane transcript isn't available should you use the canonical transcript?
ensembl mane gnomad canonical
12 months ago by amy__ ▴ 250
0
votes
1
reply
574
views
LOFTEE flag on GnomAD - END_TRUNC
loftee gnomad
updated 13 months ago by 165k • written 13 months ago by ▴ 250
0
votes
1
reply
460
views
Extracting LOF variants and incidence from GnomAD for a list of genes
Gnomad LOF genes
updated 14 months ago by 4.5k • written 14 months ago by ▴ 250
2
votes
6
replies
1.4k
views
Genotypes in vcf files
genotypes vcf
updated 15 months ago by 23k • written 15 months ago by ▴ 250
0
votes
0
replies
422
views
Filtering vcf by strand bias / annotating strand bias on
Vcf
updated 16 months ago by 45k • written 16 months ago by ▴ 250
0
votes
1
reply
567
views
How to find the most representative protein data base ID for your protein?
modelling protein database
updated 17 months ago by 149k • written 17 months ago by ▴ 250
1
vote
3
replies
768
views
Classification for low quality variant on IGV
bam igv
updated 19 months ago by ★ 2.9k • written 19 months ago by ▴ 250
6
votes
2
replies
1.4k
views
IGV - is it possible to tell what allele a read is from?
WES reads IGV
20 months ago by amy__ ▴ 250
1
vote
2
replies
694
views
Low coverage in specific exons of genes - sequencing errors?
coverage
20 months ago by amy__ ▴ 250
1
vote
4
replies
1.2k
views
Difference between USCS exon coordinates and ensembl
exons Ensembl
21 months ago by amy__ ▴ 250
0
votes
0
replies
498
views
GC content of WES cohort
WES FASTQC GC-content
updated 22 months ago by 45k • written 22 months ago by ▴ 250
1
vote
1
reply
667
views
Variant depth cut off - justification
VCF depth variant
updated 23 months ago by ★ 2.9k • written 23 months ago by ▴ 250
4
votes
3
replies
972
views
Is it possible to do bedtools multicov across the entire genome?
bedtools
updated 21 months ago by 45k • written 2.1 years ago by ▴ 250
0
votes
0
replies
496
views
Haloplex HS - should you remove duplicates?
deduplicate Haloplex duplicates
2.1 years ago by amy__ ▴ 250
3
votes
3
replies
1.1k
views
liftover output column help
liftover
updated 2.2 years ago by 165k • written 2.2 years ago by ▴ 250
0
votes
0
replies
378
views
GQ score - what do the numbers mean? How can this be interpreted?
vcf GQ
2.4 years ago by amy__ ▴ 250
0
votes
3
replies
789
views
Add absolute colours to heat map depending on range
heatmap pheatmap
updated 2.4 years ago by 5.0k • written 2.4 years ago by ▴ 250
3
votes
3
replies
2.4k
views
bcftools split-vep -- how to split the INFO column up and also assign the ensembl vep headers
bcftools ensembl-vep vep
updated 21 months ago by 45k • written 2.5 years ago by ▴ 250
0
votes
6
replies
1.7k
views
Missing reads in fastp
fastp filtering trimming
updated 2.6 years ago by 102k • written 2.6 years ago by ▴ 250
18
votes
12
replies
8.3k
views
6 follow
Which hg38 file?
reference hg38 NCBI
updated 19 months ago by 87k • written 2.6 years ago by ▴ 250
0
votes
15
replies
2.8k
views
Chromosome accession numbers correspond to which chromosome?
bam chromosome bed
2.4 years ago by amy__ ▴ 250
1
vote
2
replies
4.3k
views
fastp ERROR: igzip: encountered while decompressing file:
fastp igzip trimming
updated 2.7 years ago by 149k • written 2.7 years ago by ▴ 250
3
votes
5
replies
2.3k
views
qualimap - bed file error - BED format error, there should be at least 6 fields.
qualimap
updated 2.8 years ago by 36k • written 2.8 years ago by ▴ 250
2
votes
3
replies
1.8k
views
bedcov output meaning
coverage read bedcov
updated 2.8 years ago by 165k • written 2.8 years ago by ▴ 250
7
votes
9
replies
2.0k
views
Do you need to define adapter sequences for trimming and QC tools?
adapters fastp illumina trimming
2.8 years ago by amy__ ▴ 250
2
votes
2
replies
784
views
Single-read mapped reads? Fastp paper unclear
fastp single-read reads
2.9 years ago by amy__ ▴ 250
9
votes
7
replies
2.3k
views
How to work out coverage (100X) of WES using exome bed file?
bed WES coverage
updated 24 months ago by 45k • written 2.9 years ago by ▴ 250
7
votes
3
replies
4.1k
views
Errors when using samtools faidx and bgzip for indexing human reference genome
bgzip samtools
updated 21 months ago by 45k • written 3.0 years ago by ▴ 250
1
vote
1
reply
761
views
Copy of FASTQC documentation pdf
fastqc documentation
updated 3.0 years ago by 102k • written 3.0 years ago by ▴ 250
0
votes
7
replies
1.8k
views
How to make a diagram of a gene?
gene diagram
updated 3.1 years ago by ★ 2.9k • written 3.1 years ago by ▴ 250
0
votes
2
replies
807
views
bwa index - failed to find .pac
index .pac hpc bwa
3.1 years ago by amy__ ▴ 250
1
vote
1
reply
1.0k
views
Input and output of picard markduplicate for deepvariant
markduplicates picard bam sam deepvariant
updated 3.2 years ago by ★ 1.8k • written 3.2 years ago by ▴ 250
0
votes
2
replies
822
views
Should your variant calling pipeline change depending on whether using WES or WGS?
calling WGS WES Variant
3.4 years ago by amy__ ▴ 250
0
votes
3
replies
1.1k
views
strange looking bcftools norm file
bcftools samtools variant
updated 21 months ago by 45k • written 4.0 years ago by ▴ 250
0
votes
7
replies
1.4k
views
subread keeps makes a weird .sam file, have i done something wrong?
subread rsubread alignment DNA reference
4.1 years ago by amy__ ▴ 250
39 results • Page 1 of 1
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