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6
votes
11
replies
3.6k
views
6 follow
User friendly (visual&interactive) VCF/BCF mining tools (2021)
gui vcf
updated 4 months ago by ▴ 10 • written 3.2 years ago by ★ 5.3k
0
votes
1
reply
573
views
Comment: Comment: Best genome browser for manual curation of gene structure(s)?
7 months ago by William ★ 5.3k
5
votes
3
replies
573
views
Best genome browser for manual curation of gene structure(s)?
structure gene
updated 7 months ago by ★ 4.0k • written 7 months ago by ★ 5.3k
0
votes
0
replies
585
views
Comment: Comment: What can cause broken read-pairs (chimeric read-pairs) in a sequencing run?
9 months ago by William ★ 5.3k
0
votes
0
replies
585
views
Comment: Comment: What can cause broken read-pairs (chimeric read-pairs) in a sequencing run?
9 months ago by William ★ 5.3k
3
votes
4
replies
585
views
What can cause broken read-pairs (chimeric read-pairs) in a sequencing run?
QC
9 months ago by William ★ 5.3k
0
votes
1
reply
684
views
Comment: Comment: Difference between mRNA and transcript record types in GFF3 and GTF
9 months ago by William ★ 5.3k
2
votes
3
replies
684
views
Difference between mRNA and transcript record types in GFF3 and GTF
gff3
updated 9 months ago by 20k • written 9 months ago by ★ 5.3k
4
votes
7
replies
3.1k
views
6 follow
Insillico dual restriction enzyme reference genome digestion.
ddradseq insillico
updated 13 months ago by ▴ 190 • written 8.4 years ago by ★ 5.3k
2
votes
2
replies
3.0k
views
Tools to create flanking sequences for variants based on a VCF file and reference genome.
vcf assay
updated 14 months ago by ▴ 10 • written 8.4 years ago by ★ 5.3k
4
votes
12
replies
4.6k
views
6 follow
Sort gff3 on chromosome, position and then featuretype (gene, mRNA, exon, CDS)
gff3
updated 14 months ago by ▴ 140 • written 4.6 years ago by ★ 5.3k
0
votes
0
replies
354
views
Find reference genome regions spanned by only mapping quality 0 reads in multiple WGS samples
mapping-quality BAM FASTA
14 months ago by William ★ 5.3k
2
votes
1
reply
609
views
Gene prediction in the era of long read sequencing data and many reference genomes
gene-prediction
17 months ago by William ★ 5.3k
1
vote
0
replies
609
views
Answer: Answer: Gene prediction in the era of long read sequencing data and many reference genom
17 months ago by William ★ 5.3k
1
vote
2
replies
5.7k
views
Comment: Comment: Is there a file format better suited for the era of pangenomics than the .vcf? W
17 months ago by William ★ 5.3k
1
vote
0
replies
810
views
Comment: Comment: Reduce poly-N regions longer than 200bp back to 200bp in a reference genome FAST
20 months ago by William ★ 5.3k
0
votes
1
reply
810
views
Comment: Comment: Reduce poly-N regions longer than 200bp back to 200bp in a reference genome FAST
20 months ago by William ★ 5.3k
3
votes
3
replies
810
views
Reduce poly-N regions longer than 200bp back to 200bp in a reference genome FASTA
FASTA poly-N
20 months ago by William ★ 5.3k
5
votes
2
replies
932
views
How to merge unique/non overlapping genes between 2 gene model GFF3 files?
gff3
updated 21 months ago by 8.9k • written 21 months ago by ★ 5.3k
0
votes
1
reply
1.2k
views
Comment: Comment: How to convert VCF (with possible predicted gene effects) to protein fasta/MSA
22 months ago by William ★ 5.3k
1
vote
3
replies
1.2k
views
How to convert VCF (with possible predicted gene effects) to protein fasta/MSA
gff3 fasta protein VCF
updated 22 months ago by 24k • written 22 months ago by ★ 5.3k
0
votes
0
replies
1000
views
Comment: Comment: How to estimate and visualize haplotype blocks on a phased VCF/BCF
22 months ago by William ★ 5.3k
1
vote
2
replies
1000
views
How to estimate and visualize haplotype blocks on a phased VCF/BCF
haplotype vcf
22 months ago by William ★ 5.3k
0
votes
0
replies
1.4k
views
Comment: Comment: how to calculate %of missing genotype in vcf file
2.2 years ago by William ★ 5.3k
0
votes
1
reply
681
views
Tool that can merge 2 VCF files while taking "representational ambiguity" of (multi-allelic) variants into account
vcf bcftools
updated 17 months ago by 44k • written 2.2 years ago by ★ 5.3k
0
votes
0
replies
424
views
How to call SVs between reference genomes and force those SVs to be genotyped in WGS samples?
SVs
2.3 years ago by William ★ 5.3k
10
votes
5
replies
7.7k
views
How to determine percentage missing genotypes in VCF/BCF?
vcf
updated 2.5 years ago by 11k • written 7.4 years ago by ★ 5.3k
28
votes
6
replies
11k
views
8 follow
Add contig lenght to VCF header in a robust way
vcf
updated 2.6 years ago by ▴ 320 • written 8.4 years ago by ★ 5.3k
0
votes
2
replies
1.5k
views
Best (GATK compatible) RadSeq/GBS pipeline in 2021
radseq gbs gatk
updated 2.7 years ago by ▴ 340 • written 3.8 years ago by ★ 5.3k
0
votes
1
reply
2.3k
views
How are features extracted and encoded from a genotype matrix / VCF file?
vcf statistics feature extraction
updated 2.8 years ago by ▴ 10 • written 8.3 years ago by ★ 5.3k
2
votes
1
reply
725
views
How does 23andme store and analyze SNP array data of 12M humans?
snparray 23andme
updated 2.8 years ago by 12k • written 2.8 years ago by ★ 5.3k
9
votes
11
replies
3.9k
views
6 follow
Forum: 2021: state and usage of compressed file standards better than BAM and FASTQ
bam compression fastq
updated 2.4 years ago by ▴ 120 • written 3.6 years ago by ★ 5.3k
0
votes
0
replies
533
views
Calculate genome regions to exclude for Structural Variant calling
SV
3.0 years ago by William ★ 5.3k
1
vote
0
replies
1.9k
views
Comment: Comment: Is it possible to construct a full genome from whole sequence VCF files containi
3.2 years ago by William ★ 5.3k
2
votes
1
reply
1.9k
views
Answer: Answer: Is it possible to construct a full genome from whole sequence VCF files containi
3.2 years ago by William ★ 5.3k
0
votes
0
replies
1.5k
views
Comment: Comment: Merging VCF files.
3.2 years ago by William ★ 5.3k
0
votes
1
reply
1.6k
views
Comment: Comment: Strange speed up in GATK LeftAlignIndels
3.2 years ago by William ★ 5.3k
0
votes
1
reply
1.6k
views
Answer: Answer: Strange speed up in GATK LeftAlignIndels
3.2 years ago by William ★ 5.3k
1
vote
1
reply
937
views
Filter criteria for variants based on GBS data
gbs filter
updated 3.2 years ago by ★ 2.2k • written 3.2 years ago by ★ 5.3k
1
vote
0
replies
5.0k
views
Answer: Answer: How to merge many huge gVCFs with high speed.
3.2 years ago by William ★ 5.3k
0
votes
0
replies
3.6k
views
Comment: Comment: User friendly (visual&interactive) VCF/BCF mining tools (2021)
3.2 years ago by William ★ 5.3k
0
votes
0
replies
3.6k
views
Comment: Comment: User friendly (visual&interactive) VCF/BCF mining tools (2021)
3.2 years ago by William ★ 5.3k
0
votes
1
reply
3.6k
views
Comment: Comment: User friendly (visual&interactive) VCF/BCF mining tools (2021)
3.2 years ago by William ★ 5.3k
0
votes
0
replies
3.9k
views
Comment: Comment: How to set variant FILTER in a VCF file based on overlap with regions in a BED
3.3 years ago by William ★ 5.3k
0
votes
0
replies
985
views
Comment: Comment: Wobbly average GC profile spanning entire read length; what the cause and is it
3.4 years ago by William ★ 5.3k
0
votes
2
replies
985
views
Wobbly average GC profile spanning entire R1 read length; what the cause and is it bad
fastq qc
3.4 years ago by William ★ 5.3k
0
votes
0
replies
1.5k
views
Comment: Comment: Best pre and post alignment / variant calling QC tools for many WGS/RNA samples
3.4 years ago by William ★ 5.3k
3
votes
3
replies
1.5k
views
Best pre and post alignment / variant calling QC tools for many WGS/RNA samples 2021
fastq vcf bam
3.4 years ago by William ★ 5.3k
47
votes
22
replies
36k
views
17 follow
Multi-Sample Vcf To Phylogenetic Tree.
vcf
updated 5 months ago by • 0 • written 11.1 years ago by ★ 5.3k
0
votes
1
reply
3.9k
views
Comment: Comment: 2021: state and usuge of compressed file standards better than BAM and FASTQ
3.6 years ago by William ★ 5.3k
385 results • Page 1 of 8
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