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0
votes
7
replies
505
views
Is it possible to query column of particular sample on VCF?
vcf
8 weeks ago by optimistsso4co3 ▴ 90
3
votes
6
replies
445
views
How to filter VCF for only variants present in particular sample?
vcf
8 weeks ago by optimistsso4co3 ▴ 90
1
vote
2
replies
271
views
Is it possible to annotate each person individually with VEP?
VEP
updated 8 weeks ago by 810 • written 8 weeks ago by ▴ 90
1
vote
1
reply
191
views
Is there a tool to standartise ANY kind of human variant list file? (like vcf, plink, 23andMe etc)
23andme
updated 9 weeks ago by 2.3k • written 9 weeks ago by ▴ 90
0
votes
1
reply
218
views
Where to find Structural variant database dgvMerged for ANNOVAR?
annovar
9 weeks ago by optimistsso4co3 ▴ 90
0
votes
0
replies
215
views
How to control number of cores GATK can use?
gatk
3 months ago by optimistsso4co3 ▴ 90
0
votes
0
replies
222
views
Do you have to select "pulled" or "final" bam in MELT mobile element discovery step of genotyping?
melt
3 months ago by optimistsso4co3 ▴ 90
0
votes
2
replies
301
views
Mobile element discovery with MELT brings different results when chromosomes are analysed separate
melt
3 months ago by optimistsso4co3 ▴ 90
1
vote
1
reply
210
views
Is it possible to add variant type "VT" to each variant in vcf?
bcftools
updated 4 months ago by 37k • written 4 months ago by ▴ 90
0
votes
3
replies
262
views
gatk requests enormous amounts of memory. How to limit it?
gatk
updated 4 months ago by ▴ 780 • written 4 months ago by ▴ 90
0
votes
0
replies
183
views
How to extract region from GVCF file?
GVCF
5 months ago by optimistsso4co3 ▴ 90
1
vote
1
reply
183
views
How to calculate indels per individual?
vcf
updated 7 months ago by 149k • written 7 months ago by ▴ 90
1
vote
1
reply
427
views
How to prepare vcf for use with Picard?
picard
updated 8 months ago by 149k • written 8 months ago by ▴ 90
0
votes
0
replies
201
views
How to fill vcf ALT field for sites where it's missing?
vcf
8 months ago by optimistsso4co3 ▴ 90
2
votes
2
replies
339
views
How to correct for allele frequency mismatches?
plink
8 months ago by optimistsso4co3 ▴ 90
6
votes
10
replies
826
views
Why isn't it a common practice to call variant for every position in human genome?
ngs
updated 9 months ago by 21k • written 9 months ago by ▴ 90
0
votes
1
reply
301
views
Fastest pipeline for large scale joint genotype calling?
calling
updated 9 months ago by 149k • written 9 months ago by ▴ 90
0
votes
0
replies
222
views
Is there such thing as GVCF for structural variants allowing population genetics on SVs?
sv
9 months ago by optimistsso4co3 ▴ 90
2
votes
1
reply
271
views
How to extract specific location in .bam files
bam
updated 9 months ago by 120k • written 9 months ago by ▴ 90
0
votes
1
reply
354
views
Is it correct to merge multiple gvcf from separate variant calling?
gatk
updated 10 months ago by 21k • written 10 months ago by ▴ 90
0
votes
1
reply
404
views
Wha does combineGVCFs does to loci with variant only in gVCF from another analysis?
gatk
10 months ago by optimistsso4co3 ▴ 90
0
votes
5
replies
626
views
What are "must have" data types one should extract from WGS .fq data?
wgs
updated 10 months ago by 149k • written 10 months ago by ▴ 90
6
votes
3
replies
479
views
Is it ok to replace missing WGS calls with reference notation "0/0"?
wgs
updated 10 months ago by 149k • written 10 months ago by ▴ 90
4
votes
1
reply
1.4k
views
Can someone explain PLINK allele REF/ALT management strategy?
plink
updated 10 months ago by 9.7k • written 10 months ago by ▴ 90
2
votes
1
reply
419
views
What is the largest freely available dataset of WGS samples?
wgs
updated 11 months ago by ▴ 240 • written 11 months ago by ▴ 90
0
votes
1
reply
656
views
How to best predict effect for each variant and count specific effect found in each individual using variant effect predictor?
vcf vep
updated 12 months ago by 23k • written 12 months ago by ▴ 90
1
vote
5
replies
1.1k
views
How to pass custom software specific variables to nf-core/sarek nextflow pipeline?
wgs
updated 12 months ago by ▴ 960 • written 14 months ago by ▴ 90
4
votes
5
replies
692
views
How to paralle trim_galore for single sample?
trim_galore
updated 14 months ago by 65k • written 14 months ago by ▴ 90
0
votes
0
replies
314
views
What causes highly inflated p values of X chromosome in PLINK association analysis?
plink
22 months ago by optimistsso4co3 ▴ 90
0
votes
1
reply
622
views
Whats the format for PLINK .set file for epistasis analysis?
plink epistasis .set
updated 23 months ago by 9.7k • written 23 months ago by ▴ 90
0
votes
2
replies
478
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
2.4 years ago by optimistsso4co3 ▴ 90
0
votes
1
reply
500
views
How to save SNPs removed by quality control? Plink
plink
2.5 years ago by optimistsso4co3 ▴ 90
3
votes
3
replies
1.2k
views
Whats the point of genotype pruning before imputation?
imputation plink --indep-pariwise r2
3.2 years ago by optimistsso4co3 ▴ 90
33 results • Page 1 of 1
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