User: bari.ballew
bari.ballew • 260
- Reputation:
- 260
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- Trusted
- Location:
- USA/NIH
- Twitter:
- @BariBallew
- Last seen:
- 2 months ago
- Joined:
- 3 years, 1 month ago
- Email:
- b**********@gmail.com
Posts by bari.ballew
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... I am delighted to announce TWO PhD-level #bioinformatics openings on my team!
Do you get up-in-arms about ancestry inference? Does the loss of uncertainty when converting imputed probabilities to genotypes keep you up at night? Do you have strong opinions about the minimum size of a dataset that w ...
written 3 months ago by
bari.ballew • 260
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... Do you want to follow your passion for GWAS, while building your skills in other bioinformatics analyses? Come join my supportive and enthusiastic team of bioinformaticians! We have opportunities to get your hands dirty with GWAS and meta-analysis, WES/WGS, RNA-seq, metagenomics, structural variatio ...
written 4 months ago by
bari.ballew • 260
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... You can force-call over a set of alleles with HaplotypeCaller. Look at the flags --force-call-filtered-alleles and --alleles. ...
written 6 months ago by
bari.ballew • 260
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... Sure! As the Perl programmers say, TIMTOWTDI!
It's because of the different number of characters. sample_9 has one less character than the other samples, so it hits the default tab spacing differently. ...
written 6 months ago by
bari.ballew • 260
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... Hi there! First, your sample file needs to be formatted like this: `sample_namepath/to/sample.vcf`
If you have multi-sample VCFs (or gVCFs), you can generate a list of samples in each VCF using bcftools like this:
n=$(bcftools query -l );'
echo "${n}\t" > sample.map
For multiple VCFs, ...
written 6 months ago by
bari.ballew • 260
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... Can you post the header of your vcf? ...
written 10 months ago by
bari.ballew • 260
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... There are numerous ways to do this, many of which are described here: [https://www.biostars.org/p/98582/][1]
[1]: https://www.biostars.org/p/98582/ ...
written 10 months ago by
bari.ballew • 260
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... If you're looking at a driver mutation, you can use the very rough back-of-the-envelope comparison to the estimated tumor purity. E.g., if a driver deletion is being reported at ~20% variant allele fraction in a sample that a pathologist determined was 40% tumor, this suggests the deletion affects ...
written 12 months ago by
bari.ballew • 260
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... The answer will depend on your experimental design and the hypotheses you are testing.
If, for example, you have cases and controls in both batches, and you want to run a pairwise burden test to determine whether cases are enriched/depleted for variation in certain genes, then you ought to run th ...
written 12 months ago by
bari.ballew • 260
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... Try altering chr11_snp_pos.txt to have a single tab-delimited position per line, as described in the vcftools documentation. E.g.:
1195855385
1172496148
Are there two different alt alleles at position 11:72496148? That could result in more than one line for a single position in the VCF. ...
written 17 months ago by
bari.ballew • 260
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10 months ago,
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For A: tool to detect large deletions
Scholar
18 months ago,
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For A: tool to detect large deletions
Scholar
18 months ago,
created an answer that has been accepted.
For A: tool to detect large deletions
Teacher
18 months ago,
created an answer with at least 3 up-votes.
For A: tool to detect large deletions
Teacher
18 months ago,
created an answer with at least 3 up-votes.
For A: tool to detect large deletions
Scholar
22 months ago,
created an answer that has been accepted.
For A: tool to detect large deletions
Teacher
22 months ago,
created an answer with at least 3 up-votes.
For A: tool to detect large deletions
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