User: bdolin

gravatar for bdolin
bdolin90
Reputation:
90
Status:
Trusted
Location:
Elimu Informatics
Website:
http://www.elimu.io/
Last seen:
1 month, 1 week ago
Joined:
1 year, 2 months ago
Email:
b*****@elimu.io

Posts by bdolin

<prev • 28 results • page 1 of 3 • next >
0
votes
0
answers
122
views
0
answers
Is there SAM/VCF-to-FHIR translation software?
... Greetings, Is anyone aware of software that can convert 'raw' genetics data (e.g. FASTQ/SAM/VCF) into HL7 FHIR format? (The only one I'm aware of is 'FHIR-converter' [https://github.com/engenomics/deprecated-fhir-converter]). Thanks ...
sequencing written 7 weeks ago by bdolin90
0
votes
3
answers
205
views
3
answers
Answer: A: How can I convert VCF to HGVS format?
... You may also be interested in this: https://batch.variantvalidator.org/vcf2hgvs/ From what I've seen, there are a number of VCF to HGVS converters, and they generally only look at a few VCF fields (e.g. Chr, Pos, Ref, Alt), so have some limitations. ...
written 9 weeks ago by bdolin90
0
votes
2
answers
293
views
2
answers
Comment: C: Help understanding CHROM and POS fields in VCF
... Here is where I took the example from: http://www.internationalgenome.org/wiki/Analysis/vcf4.0/ ...
written 6 months ago by bdolin90
0
votes
2
answers
293
views
2
answers
Comment: C: Help understanding CHROM and POS fields in VCF
... Thank you for your answer. If VCF Pos=14370, how can it be that corresponding HGVS has position 66370? ...
written 6 months ago by bdolin90
1
vote
2
answers
293
views
2
answers
Help understanding CHROM and POS fields in VCF
... Greetings, Can someone explain how to relate CHROM and POS in VCF to the corresponding position in the referenced dbSNP? For instance, in the following example: #CHROM POS ID REF ALT 20 14370 rs6054257 G A It looks as though the VCF is referring to a variant on Chr2 ...
genome sequence written 6 months ago by bdolin90 • updated 6 months ago by finswimmer3.6k
1
vote
0
answers
413
views
0
answers
Tutorial: Fall 2017 Introduction to Human Genomics for Clinical Informaticists
... Greetings, The Fall 2017 session of our "Introduction to Human Genomics for Clinical Informaticists" course has completed, and I thought some of you might be interested in the materials. This is an academic course designed for clinical informaticists with little or distant genetics education and w ...
genome tutorial written 6 months ago by bdolin90
0
votes
1
answer
342
views
1
answers
Comment: C: Help understanding PrecisionFDA and GA4GH "TRUTH.TP" and "QUERY.TP" metrics
... Thank you jzook. That was exactly the piece that I needed to understand. ...
written 7 months ago by bdolin90
0
votes
1
answer
342
views
1
answers
Comment: C: Help understanding PrecisionFDA and GA4GH "TRUTH.TP" and "QUERY.TP" metrics
... Thank you Kevin, I think I'm getting it! :-) Here are definitions from the above sites: True Positive in Truth (**TRUTH.TP**): a site in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site... True Positive in Query (**Q ...
written 7 months ago by bdolin90 • updated 7 months ago by Kevin Blighe24k
0
votes
1
answer
342
views
1
answer
Help understanding PrecisionFDA and GA4GH "TRUTH.TP" and "QUERY.TP" metrics
... Greetings, GA4GH benchmarking performance metrics (https://github.com/ga4gh/benchmarking-tools/blob/update-perf-metrics-definitions/doc/standards/GA4GHBenchmarkingPerformanceMetricsDefinitions.md) and PrecisionFDA Truth Challenge (https://precision.fda.gov/challenges/truth/results) define a "Truth. ...
next-gen sequence written 7 months ago by bdolin90 • updated 7 months ago by jzook0
0
votes
1
answer
361
views
1
answers
Answer: A: HGVS for F8 Intron 22 inversion (revisited)
... A response I received from the HGVS/HVP/HUGO sequence variant description working group: ---------- *acc. to HGVS recommendations the description is correct. It states that there is an inversion on the X chromosome with, based on the NC_000023.10 reference sequence, the breakpoints between nucleo ...
written 9 months ago by bdolin90

Latest awards to bdolin

Appreciated 11 months ago, created a post with more than 5 votes. For Introduction to Human Genomics for Clinical Informaticists

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 547 users visited in the last hour