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402
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Protocol to combine WGS with Nanopore for Structural Variant confirmation?
wgs
updated 7 weeks ago by ★ 1.9k • written 7 weeks ago by ▴ 110
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0
replies
268
views
Normalisation of PLINK/VCF files?
plink
5 months ago by optimistsso4co3 ▴ 110
0
votes
0
replies
380
views
Guide for ICD-10 to EFO conversion?
icd10 efo
6 months ago by optimistsso4co3 ▴ 110
0
votes
2
replies
646
views
Don't see uploaded files for linking in EGA (European Genome Archive)
EGA
11 months ago by optimistsso4co3 ▴ 110
2
votes
1
reply
857
views
How to Remove Phasing Information from a VCF File?
phasing
updated 11 months ago by 161k • written 11 months ago by ▴ 110
3
votes
6
replies
1.9k
views
Singularity image is not working in nextflow
nextflow singularity
updated 12 months ago by 81k • written 12 months ago by ▴ 110
0
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0
replies
275
views
Is there a array-based population dataset with phenotypes like eye colour available?
gwas
13 months ago by optimistsso4co3 ▴ 110
2
votes
1
reply
501
views
fastQC - how to know if sample is good quality ?
fastqc
updated 13 months ago by 43k • written 13 months ago by ▴ 110
0
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0
replies
431
views
Protocol to detect chromosomal ploidy from WGS VCF?
wgs ploidy
14 months ago by optimistsso4co3 ▴ 110
0
votes
2
replies
589
views
Can you apply Base Score Recalibration in parallel?
wgs
updated 14 months ago by 3.9k • written 14 months ago by ▴ 110
0
votes
3
replies
759
views
How to interpret deletion the length of chromosome?
del
updated 15 months ago by 161k • written 15 months ago by ▴ 110
0
votes
7
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1.0k
views
Is it possible to query column of particular sample on VCF?
vcf
20 months ago by optimistsso4co3 ▴ 110
3
votes
6
replies
1.2k
views
How to filter VCF for only variants present in particular sample?
vcf
20 months ago by optimistsso4co3 ▴ 110
1
vote
2
replies
550
views
Is it possible to annotate each person individually with VEP?
VEP
updated 21 months ago by 3.9k • written 21 months ago by ▴ 110
1
vote
1
reply
442
views
Is there a tool to standartise ANY kind of human variant list file? (like vcf, plink, 23andMe etc)
23andme
updated 21 months ago by 2.8k • written 21 months ago by ▴ 110
0
votes
1
reply
550
views
Where to find Structural variant database dgvMerged for ANNOVAR?
annovar
21 months ago by optimistsso4co3 ▴ 110
0
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0
replies
384
views
How to control number of cores GATK can use?
gatk
22 months ago by optimistsso4co3 ▴ 110
0
votes
0
replies
436
views
Do you have to select "pulled" or "final" bam in MELT mobile element discovery step of genotyping?
melt
22 months ago by optimistsso4co3 ▴ 110
0
votes
2
replies
615
views
Mobile element discovery with MELT brings different results when chromosomes are analysed separate
melt
22 months ago by optimistsso4co3 ▴ 110
1
vote
1
reply
602
views
Is it possible to add variant type "VT" to each variant in vcf?
bcftools
updated 23 months ago by 43k • written 23 months ago by ▴ 110
0
votes
3
replies
591
views
gatk requests enormous amounts of memory. How to limit it?
gatk
updated 23 months ago by ▴ 830 • written 23 months ago by ▴ 110
0
votes
0
replies
433
views
How to extract region from GVCF file?
GVCF
24 months ago by optimistsso4co3 ▴ 110
1
vote
1
reply
420
views
How to calculate indels per individual?
vcf
updated 2.2 years ago by 161k • written 2.2 years ago by ▴ 110
1
vote
1
reply
1.0k
views
How to prepare vcf for use with Picard?
picard
updated 2.2 years ago by 161k • written 2.2 years ago by ▴ 110
0
votes
0
replies
418
views
How to fill vcf ALT field for sites where it's missing?
vcf
2.3 years ago by optimistsso4co3 ▴ 110
2
votes
2
replies
740
views
How to correct for allele frequency mismatches?
plink
2.2 years ago by optimistsso4co3 ▴ 110
6
votes
10
replies
1.6k
views
Why isn't it a common practice to call variant for every position in human genome?
ngs
updated 2.3 years ago by 22k • written 2.3 years ago by ▴ 110
0
votes
1
reply
577
views
Fastest pipeline for large scale joint genotype calling?
calling
updated 2.4 years ago by 161k • written 2.4 years ago by ▴ 110
0
votes
0
replies
448
views
Is there such thing as GVCF for structural variants allowing population genetics on SVs?
sv
2.4 years ago by optimistsso4co3 ▴ 110
2
votes
1
reply
495
views
How to extract specific location in .bam files
bam
updated 2.4 years ago by 141k • written 2.4 years ago by ▴ 110
0
votes
1
reply
665
views
Is it correct to merge multiple gvcf from separate variant calling?
gatk
updated 2.4 years ago by 22k • written 2.4 years ago by ▴ 110
0
votes
1
reply
742
views
Wha does combineGVCFs does to loci with variant only in gVCF from another analysis?
gatk
2.4 years ago by optimistsso4co3 ▴ 110
0
votes
5
replies
1.2k
views
What are "must have" data types one should extract from WGS .fq data?
wgs
updated 2.5 years ago by 161k • written 2.5 years ago by ▴ 110
6
votes
3
replies
809
views
Is it ok to replace missing WGS calls with reference notation "0/0"?
wgs
updated 2.5 years ago by 161k • written 2.5 years ago by ▴ 110
6
votes
1
reply
3.7k
views
Can someone explain PLINK allele REF/ALT management strategy?
plink
updated 2.5 years ago by 10k • written 2.5 years ago by ▴ 110
2
votes
1
reply
668
views
What is the largest freely available dataset of WGS samples?
wgs
updated 2.5 years ago by ▴ 250 • written 2.5 years ago by ▴ 110
0
votes
1
reply
979
views
How to best predict effect for each variant and count specific effect found in each individual using variant effect predictor?
vcf vep
updated 2.6 years ago by 23k • written 2.6 years ago by ▴ 110
2
votes
5
replies
1.9k
views
How to pass custom software specific variables to nf-core/sarek nextflow pipeline?
wgs
updated 2.6 years ago by ★ 1.4k • written 2.8 years ago by ▴ 110
4
votes
5
replies
1.2k
views
How to paralle trim_galore for single sample?
trim_galore
updated 2.8 years ago by 81k • written 2.8 years ago by ▴ 110
0
votes
0
replies
489
views
What causes highly inflated p values of X chromosome in PLINK association analysis?
plink
3.4 years ago by optimistsso4co3 ▴ 110
0
votes
1
reply
917
views
Whats the format for PLINK .set file for epistasis analysis?
plink epistasis .set
updated 3.5 years ago by 10k • written 3.5 years ago by ▴ 110
0
votes
2
replies
709
views
What's the probability of genotype error at the end of 10 repeated A variants? Given low coverage sequencing of 1000G phase 1
sequencing error
3.9 years ago by optimistsso4co3 ▴ 110
0
votes
1
reply
707
views
How to save SNPs removed by quality control? Plink
plink
4.1 years ago by optimistsso4co3 ▴ 110
3
votes
3
replies
1.6k
views
Whats the point of genotype pruning before imputation?
imputation plink --indep-pariwise r2
4.8 years ago by optimistsso4co3 ▴ 110
44 results • Page 1 of 1
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