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0
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7
replies
387
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Is it possible to query column of particular sample on VCF?
vcf
18 days ago by optimistsso4co3 ▴ 90
0
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0
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387
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Answer: Answer: Is it possible to query column of particular sample on VCF?
18 days ago by optimistsso4co3 ▴ 90
3
votes
6
replies
332
views
How to filter VCF for only variants present in particular sample?
vcf
18 days ago by optimistsso4co3 ▴ 90
1
vote
0
replies
332
views
Answer: Answer: How to filter VCF for only variants present in particular sample?
18 days ago by optimistsso4co3 ▴ 90
0
votes
0
replies
332
views
Comment: Comment: How to filter VCF for only variants present in particular sample?
18 days ago by optimistsso4co3 ▴ 90
0
votes
1
reply
332
views
Comment: Comment: How to filter VCF for only variants present in particular sample?
18 days ago by optimistsso4co3 ▴ 90
0
votes
1
reply
332
views
Answer: Answer: How to filter VCF for only variants present in particular sample?
18 days ago by optimistsso4co3 ▴ 90
0
votes
0
replies
387
views
Comment: Comment: Is it possible to query column of particular sample on VCF?
18 days ago by optimistsso4co3 ▴ 90
0
votes
1
reply
387
views
Comment: Comment: Is it possible to query column of particular sample on VCF?
18 days ago by optimistsso4co3 ▴ 90
0
votes
1
reply
387
views
Comment: Comment: Is it possible to query column of particular sample on VCF?
18 days ago by optimistsso4co3 ▴ 90
1
vote
2
replies
223
views
Is it possible to annotate each person individually with VEP?
VEP
updated 20 days ago by 660 • written 20 days ago by ▴ 90
1
vote
1
reply
165
views
Is there a tool to standartise ANY kind of human variant list file? (like vcf, plink, 23andMe etc)
23andme
updated 28 days ago by 2.2k • written 29 days ago by ▴ 90
0
votes
1
reply
178
views
Where to find Structural variant database dgvMerged for ANNOVAR?
annovar
4 weeks ago by optimistsso4co3 ▴ 90
0
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0
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178
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Answer: Answer: Where to find Structural variant database dgvMerged for ANNOVAR?
4 weeks ago by optimistsso4co3 ▴ 90
0
votes
0
replies
201
views
How to control number of cores GATK can use?
gatk
8 weeks ago by optimistsso4co3 ▴ 90
0
votes
0
replies
396
views
Comment: Comment: Research Scientist (Fungal & Algal Program)
10 weeks ago by optimistsso4co3 ▴ 90
0
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0
replies
210
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Do you have to select "pulled" or "final" bam in MELT mobile element discovery step of genotyping?
melt
10 weeks ago by optimistsso4co3 ▴ 90
0
votes
0
replies
275
views
Comment: Comment: Mobile element discovery with MELT brings different results when chromosomes are
11 weeks ago by optimistsso4co3 ▴ 90
0
votes
2
replies
275
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Mobile element discovery with MELT brings different results when chromosomes are analysed separate
melt
11 weeks ago by optimistsso4co3 ▴ 90
1
vote
1
reply
193
views
Is it possible to add variant type "VT" to each variant in vcf?
bcftools
updated 3 months ago by 36k • written 3 months ago by ▴ 90
0
votes
3
replies
241
views
gatk requests enormous amounts of memory. How to limit it?
gatk
updated 3 months ago by ▴ 740 • written 3 months ago by ▴ 90
0
votes
0
replies
170
views
How to extract region from GVCF file?
GVCF
3 months ago by optimistsso4co3 ▴ 90
1
vote
1
reply
173
views
How to calculate indels per individual?
vcf
updated 6 months ago by 148k • written 6 months ago by ▴ 90
1
vote
1
reply
381
views
How to prepare vcf for use with Picard?
picard
updated 6 months ago by 148k • written 6 months ago by ▴ 90
0
votes
0
replies
191
views
How to fill vcf ALT field for sites where it's missing?
vcf
7 months ago by optimistsso4co3 ▴ 90
0
votes
0
replies
320
views
Comment: Comment: How to correct for allele frequency mismatches?
6 months ago by optimistsso4co3 ▴ 90
2
votes
2
replies
320
views
How to correct for allele frequency mismatches?
plink
6 months ago by optimistsso4co3 ▴ 90
6
votes
10
replies
791
views
Why isn't it a common practice to call variant for every position in human genome?
ngs
updated 8 months ago by 20k • written 8 months ago by ▴ 90
1
vote
0
replies
791
views
Comment: Comment: Why isn't it a common practice to call variant for every position in human genom
8 months ago by optimistsso4co3 ▴ 90
0
votes
0
replies
791
views
Comment: Comment: Why isn't it a common practice to call variant for every position in human genom
8 months ago by optimistsso4co3 ▴ 90
0
votes
1
reply
791
views
Comment: Comment: Why isn't it a common practice to call variant for every position in human genom
8 months ago by optimistsso4co3 ▴ 90
0
votes
1
reply
791
views
Comment: Comment: Why isn't it a common practice to call variant for every position in human genom
8 months ago by optimistsso4co3 ▴ 90
0
votes
1
reply
281
views
Fastest pipeline for large scale joint genotype calling?
calling
updated 8 months ago by 148k • written 8 months ago by ▴ 90
0
votes
0
replies
211
views
Is there such thing as GVCF for structural variants allowing population genetics on SVs?
sv
8 months ago by optimistsso4co3 ▴ 90
2
votes
1
reply
258
views
How to extract specific location in .bam files
bam
updated 8 months ago by 119k • written 8 months ago by ▴ 90
0
votes
1
reply
334
views
Is it correct to merge multiple gvcf from separate variant calling?
gatk
updated 9 months ago by 20k • written 9 months ago by ▴ 90
0
votes
0
replies
392
views
Comment: Comment: Wha does combineGVCFs does to loci with variant only in gVCF from another analys
9 months ago by optimistsso4co3 ▴ 90
0
votes
1
reply
392
views
Wha does combineGVCFs does to loci with variant only in gVCF from another analysis?
gatk
9 months ago by optimistsso4co3 ▴ 90
0
votes
1
reply
605
views
Comment: Comment: What are "must have" data types one should extract from WGS .fq data?
9 months ago by optimistsso4co3 ▴ 90
0
votes
1
reply
605
views
Comment: Comment: What are "must have" data types one should extract from WGS .fq data?
9 months ago by optimistsso4co3 ▴ 90
0
votes
5
replies
605
views
What are "must have" data types one should extract from WGS .fq data?
wgs
updated 9 months ago by 148k • written 9 months ago by ▴ 90
0
votes
1
reply
460
views
Comment: Comment: Is it ok to replace missing WGS calls with reference notation "0/0"?
9 months ago by optimistsso4co3 ▴ 90
6
votes
3
replies
460
views
Is it ok to replace missing WGS calls with reference notation "0/0"?
wgs
updated 9 months ago by 148k • written 9 months ago by ▴ 90
4
votes
1
reply
1.2k
views
Can someone explain PLINK allele REF/ALT management strategy?
plink
updated 9 months ago by 9.6k • written 9 months ago by ▴ 90
2
votes
1
reply
405
views
What is the largest freely available dataset of WGS samples?
wgs
updated 9 months ago by ▴ 230 • written 9 months ago by ▴ 90
0
votes
1
reply
632
views
How to best predict effect for each variant and count specific effect found in each individual using variant effect predictor?
vcf vep
updated 10 months ago by 23k • written 10 months ago by ▴ 90
0
votes
1
reply
1.0k
views
Comment: Comment: How to pass custom software specific variables to nf-core/sarek nextflow pipelin
13 months ago by optimistsso4co3 ▴ 90
0
votes
2
replies
1.0k
views
Comment: Comment: How to pass custom software specific variables to nf-core/sarek nextflow pipelin
13 months ago by optimistsso4co3 ▴ 90
1
vote
5
replies
1.0k
views
How to pass custom software specific variables to nf-core/sarek nextflow pipeline?
wgs
updated 11 months ago by ▴ 920 • written 13 months ago by ▴ 90
0
votes
0
replies
671
views
Comment: Comment: How to paralle trim_galore for single sample?
13 months ago by optimistsso4co3 ▴ 90
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