User: Irene@Sequencing.com

Reputation:
200
Status:
Trusted
Location:
United States
Website:
https://sequencing.com/
Twitter:
SequencingCom
Last seen:
5 months, 2 weeks ago
Joined:
2 years, 9 months ago
Email:
g******@sequencing.com

Hola! My name is Irene and I work at Sequencing.com. My work focuses on creating bioinformatics apps that help make analysis and interpretation of genetic data more efficient. One of my current projects is aligning our open API with the GA4GH API (as we are a member of the global alliance for genomics and health organization) and also establishing Sequencing.com as a Beacon.

Posts by Irene@Sequencing.com

<prev • 32 results • page 1 of 4 • next >
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Answer: A: Can someone help me with imputation of missing SNPs using beagle 4?
... Beagle 4 has an issue if the ALT allele is not defined and instead if it is just represented by a "." when genotype is 0/0. Workaround is to use Beagle 3 or exclude rows with MAF=0. ...
written 13 months ago by Irene@Sequencing.com200
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Job: Director of Bioinformatics IT at Sequencing.com
... **Sequencing.com is growing and we're looking for innovative leaders to join our team!** **Job Description** As Director of Bioinformatics IT, you will be responsible for implementing and managing the bioinformatics IT initiatives of Sequencing.com. The Director will work collaboratively with Ex ...
bioinformatics job written 13 months ago by Irene@Sequencing.com200
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What are the best resources or tools to sort an unsorted human gVCF
... I'm trying to process a gVCF file "genome882131.hard-filtered.gvcf" and I haven't previously seen the 'hard-filtered.gvcf" extension. I simply changed the .gvcf extension to .vcf to process it. I encountered an issue using tabix on this file, however, as the data appears to be unsorted. When I tri ...
unsorted vcf gvcf genome vcf written 13 months ago by Irene@Sequencing.com200 • updated 13 months ago by ssv.bio170
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Do coordinates change between minor ref genome builds and can Liftover be used to convert minor ref genome coordinates?
... Two questions: **1) Do coordinates ever change for minor reference genome builds compared to the major reference genome build?** - For example, are coordinates for coordinates aligned to GRCh38 major reference genome always going to be the same as coordinates aligned for all minor reference genom ...
coordinates reference genomes liftover written 17 months ago by Irene@Sequencing.com200 • updated 17 months ago by Denise - Open Targets4.1k
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Comment: C: Any way to differentiate from a BAM which minor build human reference genome was
... Thanks for the info. The problem is that this isn't just one BAM file as I'm working on a universal solution regardless of what tool was used for alignment. While the contig MD5 approach may work for Picard I'm not sure if it is applicable to other common aligners. ...
written 20 months ago by Irene@Sequencing.com200
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Comment: C: Any way to differentiate from a BAM which minor build human reference genome was
... Thank you for the additional suggestion. I attempted to use a BAM file to compare against references but it looks rather tricky and appears to fall into task of reconstructing the reference from the BAM file, which I don't think can be possible in diverse range of cases (since it appears to greatly ...
written 20 months ago by Irene@Sequencing.com200
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Comment: A: Any way to differentiate from a BAM which minor build human reference genome was
... Attempted to implement Istvan's suggestion above but hit a wall and was not able to get it to work. Any other suggestions for a way to ascertain from a BAM file which minor build of the human reference genome was used to generate that BAM file? ...
written 20 months ago by Irene@Sequencing.com200
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Comment: C: Any way to differentiate from a BAM which minor build human reference genome was
... Thank you, Istvan. I've been working to implement your suggested approach but haven't yet been able to get it to work. (1) I aligned a BAM file to GRCh38.p4. (2) Tried to use this patch to determine the minor build version of this BAM file: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc ...
written 20 months ago by Irene@Sequencing.com200
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Any way to differentiate from a BAM which minor build human reference genome was used for alignment?
... If not stated in the BAM header/metadata, is there a way to ascertain from a BAM file which minor build of the human reference genome was used to generate that BAM file? I've encountered a BAM file that was aligned using a minor build of GRCh38 but I'm unable to determine which specific minor build ...
bam reference genome written 20 months ago by Irene@Sequencing.com200
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Are there any available genome data files in .AVRO format
... Are there any human genome files available for download in .AVRO format? I'm researching conversions utilizing .AVRO, such as .AVRO > .BAM or .FASTQ but so far haven't been able to find exome or WGS data in .AVRO format to work with. ...
avro written 22 months ago by Irene@Sequencing.com200 • updated 21 months ago by Biostar ♦♦ 20

Latest awards to Irene@Sequencing.com

Great Question 16 months ago, created a question with more than 5,000 views. For BWA vs Bowtie 2 (Poll)
Popular Question 17 months ago, created a question with more than 1,000 views. For How to handle chr Y data in BAM files from exome sequencing of human females
Supporter 21 months ago, voted at least 25 times.
Popular Question 2.4 years ago, created a question with more than 1,000 views. For BWA vs Bowtie 2 (Poll)
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For C: GRCH38 and hg19
Appreciated 2.5 years ago, created a post with more than 5 votes. For BWA vs Bowtie 2 (Poll)
Autobiographer 2.7 years ago, has more than 80 characters in the information field of the user's profile.

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