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94
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Fastest pipeline for large scale joint genotype calling?
calling
updated 23 hours ago by 140k • written 1 day ago by ▴ 60
0
votes
0
replies
50
views
Is there such thing as GVCF for structural variants allowing population genetics on SVs?
sv
2 days ago by optimistsso4co3 ▴ 60
2
votes
1
reply
121
views
How to extract specific location in .bam files
bam
updated 4 days ago by 110k • written 4 days ago by ▴ 60
0
votes
1
reply
127
views
Is it correct to merge multiple gvcf from separate variant calling?
gatk
updated 21 days ago by 20k • written 21 days ago by ▴ 60
0
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0
replies
222
views
Comment: Comment: Wha does combineGVCFs does to loci with variant only in gVCF from another analys
23 days ago by optimistsso4co3 ▴ 60
0
votes
1
reply
222
views
Wha does combineGVCFs does to loci with variant only in gVCF from another analysis?
gatk
23 days ago by optimistsso4co3 ▴ 60
0
votes
1
reply
359
views
Comment: Comment: What are "must have" data types one should extract from WGS .fq data?
4 weeks ago by optimistsso4co3 ▴ 60
0
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1
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359
views
Comment: Comment: What are "must have" data types one should extract from WGS .fq data?
4 weeks ago by optimistsso4co3 ▴ 60
0
votes
5
replies
359
views
What are "must have" data types one should extract from WGS .fq data?
wgs
updated 4 weeks ago by 140k • written 4 weeks ago by ▴ 60
0
votes
1
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221
views
Comment: Comment: Is it ok to replace missing WGS calls with reference notation "0/0"?
4 weeks ago by optimistsso4co3 ▴ 60
6
votes
3
replies
221
views
Is it ok to replace missing WGS calls with reference notation "0/0"?
wgs
updated 4 weeks ago by 140k • written 4 weeks ago by ▴ 60
4
votes
1
reply
207
views
Can someone explain PLINK allele REF/ALT management strategy?
plink
updated 4 weeks ago by 8.7k • written 4 weeks ago by ▴ 60
2
votes
1
reply
251
views
What is the largest freely available dataset of WGS samples?
wgs
updated 5 weeks ago by ▴ 160 • written 5 weeks ago by ▴ 60
0
votes
1
reply
437
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 weeks ago by 23k • written 10 weeks ago by ▴ 60
0
votes
1
reply
684
views
Comment: Comment: How to pass custom software specific variables to nf-core/sarek nextflow pipelin
4 months ago by optimistsso4co3 ▴ 60
0
votes
2
replies
684
views
Comment: Comment: How to pass custom software specific variables to nf-core/sarek nextflow pipelin
4 months ago by optimistsso4co3 ▴ 60
1
vote
5
replies
684
views
How to pass custom software specific variables to nf-core/sarek nextflow pipeline?
wgs
updated 12 weeks ago by ▴ 770 • written 4 months ago by ▴ 60
0
votes
0
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444
views
Comment: Comment: How to paralle trim_galore for single sample?
4 months ago by optimistsso4co3 ▴ 60
4
votes
5
replies
444
views
How to paralle trim_galore for single sample?
trim_galore
updated 4 months ago by 55k • written 4 months ago by ▴ 60
0
votes
0
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226
views
What causes highly inflated p values of X chromosome in PLINK association analysis?
plink
12 months ago by optimistsso4co3 ▴ 60
0
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1
reply
411
views
Whats the format for PLINK .set file for epistasis analysis?
plink epistasis .set
updated 14 months ago by 8.7k • written 14 months ago by ▴ 60
0
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0
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1.5k
views
Comment: C: GTEX - how to upload more than one rsIDs to get gene expression or eQTL informat
14 months ago by optimistsso4co3 ▴ 60
0
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1
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1.5k
views
Answer: A: GTEX - how to upload more than one rsIDs to get gene expression or eQTL informat
14 months ago by optimistsso4co3 ▴ 60
0
votes
2
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298
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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
18 months ago by optimistsso4co3 ▴ 60
0
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1
reply
348
views
How to save SNPs removed by quality control? Plink
plink
21 months ago by optimistsso4co3 ▴ 60
3
votes
3
replies
929
views
Whats the point of genotype pruning before imputation?
imputation plink --indep-pariwise r2
2.4 years ago by optimistsso4co3 ▴ 60
0
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0
replies
929
views
Comment: C: Whats the point of genotype pruning before imputation?
2.4 years ago by optimistsso4co3 ▴ 60
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