User: bari.ballew
bari.ballew • 230
- Reputation:
- 230
- Status:
- Trusted
- Location:
- USA/NIH
- Twitter:
- @BariBallew
- Last seen:
- an hour ago
- Joined:
- 2 years, 9 months ago
- Email:
- b**********@gmail.com
Posts by bari.ballew
<prev
• 34 results •
page 1 of 4 •
next >
0
votes
0
answers
47
views
0
answers
... 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 14 hours ago by
bari.ballew • 230
0
votes
1
answer
144
views
1
answers
... You can force-call over a set of alleles with HaplotypeCaller. Look at the flags --force-call-filtered-alleles and --alleles. ...
written 9 weeks ago by
bari.ballew • 230
0
votes
1
answer
243
views
1
answers
... 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 9 weeks ago by
bari.ballew • 230
1
vote
1
answer
243
views
1
answers
... 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 10 weeks ago by
bari.ballew • 230
0
votes
0
answers
109
views
0
answers
... Can you post the header of your vcf? ...
written 5 months ago by
bari.ballew • 230
1
vote
1
answer
206
views
1
answers
... 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 5 months ago by
bari.ballew • 230
2
votes
1
answer
178
views
1
answers
... 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 8 months ago by
bari.ballew • 230
0
votes
1
answer
463
views
1
answers
... 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 8 months ago by
bari.ballew • 230
0
votes
1
answer
249
views
1
answers
... 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 13 months ago by
bari.ballew • 230
1
vote
1
answer
1.3k
views
1
answers
... FastQC names output files by taking the original filename, removing the `.fastq` extension, and replacing the extension with `_fastqc.html` or `_fastqc.zip`. So, your output should be `reports/{sample}.trimmed_fastq.html` and `reports/{sample}.trimmed_fastq.zip`
Also, you only need to include the ...
written 13 months ago by
bari.ballew • 230
Latest awards to bari.ballew
Scholar
5 months ago,
created an answer that has been accepted.
For A: tool to detect large deletions
Scholar
14 months ago,
created an answer that has been accepted.
For A: tool to detect large deletions
Scholar
14 months ago,
created an answer that has been accepted.
For A: tool to detect large deletions
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: tool to detect large deletions
Teacher
14 months ago,
created an answer with at least 3 up-votes.
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
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 2017 users visited in the last hour