User: bari.ballew

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bari.ballew230
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@BariBallew
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Posts by bari.ballew

<prev • 34 results • page 1 of 4 • next >
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Job: GWAS Bioinformatician at the Cancer Genomics Research Lab, National Cancer Institute - MD, USA
... 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 ...
gwas assocation job written 14 hours ago by bari.ballew230
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Answer: A: Genotyping samples at a predetermined list of locations
... 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.ballew230
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Comment: C: GATK GenomicsDBImport - use list as input
... 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.ballew230
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Answer: A: GATK GenomicsDBImport - use list as input
... 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.ballew230
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Comment: C: illumina variant interpreter vcf format version error
... Can you post the header of your vcf? ...
written 5 months ago by bari.ballew230
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Answer: A: Rename Chromosome position/Notation in VCF file
... 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.ballew230
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Answer: A: Identifying zygosity of somatic deletion
... 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.ballew230
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Answer: A: Are there any issues with using sample reads coming from different technologies
... 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.ballew230
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Answer: A: Selecting set of SNPs using vcftools
... 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.ballew230
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Answer: A: Snakemake FastQC MissingOutputFiles ErrorM
... 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.ballew230

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

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