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0
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3
replies
1.0k
views
Protocol to combine WGS with Nanopore for Structural Variant confirmation?
wgs
updated 20 months ago by ★ 2.0k • written 20 months ago by ▴ 140
0
votes
0
replies
509
views
Normalisation of PLINK/VCF files?
plink
2.0 years ago by optimistsso4co3 ▴ 140
0
votes
0
replies
780
views
Guide for ICD-10 to EFO conversion?
icd10 efo
2.1 years ago by optimistsso4co3 ▴ 140
0
votes
2
replies
1.4k
views
Don't see uploaded files for linking in EGA (European Genome Archive)
EGA
2.5 years ago by optimistsso4co3 ▴ 140
2
votes
2
replies
1.8k
views
How to Remove Phasing Information from a VCF File?
phasing
updated 3 months ago by • 0 • written 2.5 years ago by ▴ 140
3
votes
6
replies
4.0k
views
Singularity image is not working in nextflow
nextflow singularity
updated 2.6 years ago by 90k • written 2.6 years ago by ▴ 140
0
votes
0
replies
476
views
Is there a array-based population dataset with phenotypes like eye colour available?
gwas
2.7 years ago by optimistsso4co3 ▴ 140
2
votes
1
reply
873
views
fastQC - how to know if sample is good quality ?
fastqc
updated 2.7 years ago by 45k • written 2.7 years ago by ▴ 140
0
votes
0
replies
693
views
Protocol to detect chromosomal ploidy from WGS VCF?
wgs ploidy
2.8 years ago by optimistsso4co3 ▴ 140
0
votes
2
replies
981
views
Can you apply Base Score Recalibration in parallel?
wgs
updated 2.8 years ago by 5.2k • written 2.8 years ago by ▴ 140
0
votes
3
replies
1.3k
views
How to interpret deletion the length of chromosome?
del
updated 2.8 years ago by 166k • written 2.8 years ago by ▴ 140
0
votes
7
replies
1.9k
views
Is it possible to query column of particular sample on VCF?
vcf
3.3 years ago by optimistsso4co3 ▴ 140
4
votes
6
replies
2.2k
views
How to filter VCF for only variants present in particular sample?
vcf
3.3 years ago by optimistsso4co3 ▴ 140
1
vote
2
replies
907
views
Is it possible to annotate each person individually with VEP?
VEP
updated 3.3 years ago by 5.2k • written 3.3 years ago by ▴ 140
1
vote
1
reply
837
views
Is there a tool to standartise ANY kind of human variant list file? (like vcf, plink, 23andMe etc)
23andme
updated 3.3 years ago by 2.9k • written 3.3 years ago by ▴ 140
0
votes
1
reply
934
views
Where to find Structural variant database dgvMerged for ANNOVAR?
annovar
3.3 years ago by optimistsso4co3 ▴ 140
0
votes
0
replies
590
views
How to control number of cores GATK can use?
gatk
3.4 years ago by optimistsso4co3 ▴ 140
0
votes
1
reply
842
views
Do you have to select "pulled" or "final" bam in MELT mobile element discovery step of genotyping?
melt
updated 9 months ago by • 0 • written 3.4 years ago by ▴ 140
0
votes
2
replies
1.1k
views
Mobile element discovery with MELT brings different results when chromosomes are analysed separate
melt
3.4 years ago by optimistsso4co3 ▴ 140
1
vote
1
reply
1.4k
views
Is it possible to add variant type "VT" to each variant in vcf?
bcftools
updated 3.5 years ago by 45k • written 3.5 years ago by ▴ 140
0
votes
3
replies
1.1k
views
gatk requests enormous amounts of memory. How to limit it?
gatk
updated 3.5 years ago by ▴ 840 • written 3.5 years ago by ▴ 140
0
votes
0
replies
686
views
How to extract region from GVCF file?
GVCF
3.5 years ago by optimistsso4co3 ▴ 140
1
vote
1
reply
768
views
How to calculate indels per individual?
vcf
updated 3.8 years ago by 166k • written 3.8 years ago by ▴ 140
1
vote
1
reply
1.6k
views
How to prepare vcf for use with Picard?
picard
updated 3.8 years ago by 166k • written 3.8 years ago by ▴ 140
0
votes
0
replies
640
views
How to fill vcf ALT field for sites where it's missing?
vcf
3.8 years ago by optimistsso4co3 ▴ 140
2
votes
2
replies
1.7k
views
How to correct for allele frequency mismatches?
plink
3.8 years ago by optimistsso4co3 ▴ 140
6
votes
10
replies
2.8k
views
Why isn't it a common practice to call variant for every position in human genome?
ngs
updated 3.9 years ago by 23k • written 3.9 years ago by ▴ 140
0
votes
1
reply
867
views
Fastest pipeline for large scale joint genotype calling?
calling
updated 3.9 years ago by 166k • written 3.9 years ago by ▴ 140
0
votes
0
replies
713
views
Is there such thing as GVCF for structural variants allowing population genetics on SVs?
sv
3.9 years ago by optimistsso4co3 ▴ 140
2
votes
1
reply
809
views
How to extract specific location in .bam files
bam
updated 3.9 years ago by 154k • written 3.9 years ago by ▴ 140
0
votes
1
reply
964
views
Is it correct to merge multiple gvcf from separate variant calling?
gatk
updated 4.0 years ago by 23k • written 4.0 years ago by ▴ 140
0
votes
1
reply
1.1k
views
Wha does combineGVCFs does to loci with variant only in gVCF from another analysis?
gatk
4.0 years ago by optimistsso4co3 ▴ 140
0
votes
5
replies
1.9k
views
What are "must have" data types one should extract from WGS .fq data?
wgs
updated 4.0 years ago by 166k • written 4.0 years ago by ▴ 140
6
votes
3
replies
1.3k
views
Is it ok to replace missing WGS calls with reference notation "0/0"?
wgs
updated 4.0 years ago by 166k • written 4.0 years ago by ▴ 140
8
votes
1
reply
5.8k
views
Can someone explain PLINK allele REF/ALT management strategy?
plink
updated 4.0 years ago by 11k • written 4.0 years ago by ▴ 140
2
votes
1
reply
1.0k
views
What is the largest freely available dataset of WGS samples?
wgs
updated 4.0 years ago by ▴ 270 • written 4.0 years ago by ▴ 140
0
votes
1
reply
1.5k
views
How to best predict effect for each variant and count specific effect found in each individual using variant effect predictor?
vcf vep
updated 4.1 years ago by 24k • written 4.1 years ago by ▴ 140
2
votes
5
replies
3.1k
views
How to pass custom software specific variables to nf-core/sarek nextflow pipeline?
wgs
updated 4.2 years ago by ★ 1.5k • written 4.3 years ago by ▴ 140
4
votes
5
replies
1.9k
views
How to paralle trim_galore for single sample?
trim_galore
updated 4.3 years ago by 90k • written 4.3 years ago by ▴ 140
0
votes
0
replies
698
views
What causes highly inflated p values of X chromosome in PLINK association analysis?
plink
5.0 years ago by optimistsso4co3 ▴ 140
0
votes
1
reply
1.2k
views
Whats the format for PLINK .set file for epistasis analysis?
plink epistasis .set
updated 5.1 years ago by 11k • written 5.1 years ago by ▴ 140
0
votes
2
replies
1.0k
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
5.5 years ago by optimistsso4co3 ▴ 140
0
votes
1
reply
952
views
How to save SNPs removed by quality control? Plink
plink
5.7 years ago by optimistsso4co3 ▴ 140
3
votes
3
replies
2.3k
views
Whats the point of genotype pruning before imputation?
imputation plink --indep-pariwise r2
6.3 years ago by optimistsso4co3 ▴ 140
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