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6
votes
1
reply
1.6k
views
(Sanity check) Too many SNPs?
next-gen variant filter
updated 5.8 years ago by 20 • written 6.5 years ago by ▴ 70
0
votes
0
replies
1.4k
views
Using synonymous vs. non-synonymous ALT for SNP data validation
SNP alignment next-gen sequencing
6.3 years ago by rightmirem ▴ 70
0
votes
0
replies
4.6k
views
Comment: C: bcftools filter by ALT == '.'
6.3 years ago by rightmirem ▴ 70
3
votes
2
replies
4.6k
views
bcftools filter by ALT == '.'
snp next-gen sequencing sequence SNP
updated 6.3 years ago by 161k • written 6.3 years ago by ▴ 70
2
votes
2
replies
2.8k
views
HiSAT2 segfault after long run
SNP Assembly next-gen alignment
updated 6.4 years ago by 87k • written 6.4 years ago by ▴ 70
2
votes
0
replies
3.3k
views
Answer: A: Passing VCF file directly into ```HiSAT2-build --snp --haplotype```
6.4 years ago by rightmirem ▴ 70
2
votes
1
reply
3.3k
views
Passing VCF file directly into ```HiSAT2-build --snp --haplotype```
SNP snp next-gen alignment hisat2
6.4 years ago by rightmirem ▴ 70
1
vote
1
reply
2.2k
views
Comment: C: Recreating a Genomic reference (.fastq) from a BCF file
6.4 years ago by rightmirem ▴ 70
0
votes
1
reply
2.2k
views
Comment: C: Recreating a Genomic reference (.fastq) from a BCF file
6.4 years ago by rightmirem ▴ 70
4
votes
5
replies
2.2k
views
Recreating a Genomic reference (.fastq) from a BCF file
SNP Assembly snp next-gen alignment
6.4 years ago by rightmirem ▴ 70
6
votes
4
replies
1.9k
views
Faster (perhaps random) access to BAM files (for collecting statistics like average read depth)
SNP SAM BAM
updated 6.5 years ago by 6.4k • written 6.5 years ago by ▴ 70
0
votes
0
replies
1.6k
views
Comment: C: Under what circumstances does "REF | REF" (or REF / REF) show up in the VCF/BCF
6.5 years ago by rightmirem ▴ 70
0
votes
0
replies
3.8k
views
Answer: A: Unusual reports from "bcftools stats" (making me question my data)
6.5 years ago by rightmirem ▴ 70
6
votes
5
replies
3.8k
views
Unusual reports from "bcftools stats" (making me question my data)
SNP next-gen alignment software error
6.5 years ago by rightmirem ▴ 70
0
votes
1
reply
1.6k
views
Comment: C: Under what circumstances does "REF | REF" (or REF / REF) show up in the VCF/BCF
6.5 years ago by rightmirem ▴ 70
8
votes
5
replies
1.6k
views
Under what circumstances does "REF | REF" (or REF / REF) show up in the VCF/BCF file
SNP next-gen software error
updated 6.5 years ago by 47k • written 6.5 years ago by ▴ 70
1
vote
0
replies
2.3k
views
Comment: C: How to validate the OVERALL quality of a VCF/BCF file (Data munging)
6.5 years ago by rightmirem ▴ 70
1
vote
0
replies
6.8k
views
Comment: C: Understanding terms, specifically relating to GT:PL in a VCF file
6.5 years ago by rightmirem ▴ 70
0
votes
1
reply
2.3k
views
Comment: C: How to validate the OVERALL quality of a VCF/BCF file (Data munging)
6.5 years ago by rightmirem ▴ 70
0
votes
3
replies
1.2k
views
Unusual AF data (I think)
SNP genome next-gen
6.5 years ago by rightmirem ▴ 70
5
votes
4
replies
3.4k
views
What is " ./.:. " in the GT output of VCF/BCF
SNP snp next-gen BCF GT
updated 6.5 years ago by 16k • written 6.5 years ago by ▴ 70
0
votes
1
reply
3.4k
views
Answer: A: What is " ./.:. " in the GT output of VCF/BCF
6.5 years ago by rightmirem ▴ 70
4
votes
5
replies
2.3k
views
How to validate the OVERALL quality of a VCF/BCF file (Data munging)
snp SNP next-gen validation munging
updated 6.5 years ago by 87k • written 6.5 years ago by ▴ 70
14
votes
13
replies
6.8k
views
Understanding terms, specifically relating to GT:PL in a VCF file
variant sense antisense filtering terms
updated 6.5 years ago by 87k • written 6.5 years ago by ▴ 70
0
votes
1
reply
6.8k
views
Comment: C: Understanding terms, specifically relating to GT:PL in a VCF file
6.5 years ago by rightmirem ▴ 70
0
votes
1
reply
6.8k
views
Answer: A: Understanding terms, specifically relating to GT:PL in a VCF file
6.5 years ago by rightmirem ▴ 70
0
votes
1
reply
6.8k
views
Comment: C: Understanding terms, specifically relating to GT:PL in a VCF file
6.5 years ago by rightmirem ▴ 70
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