Observation
Observation
What variants are we missing when you only focus on a specific phenotype?
Research Notebook
Lab Notebook
Notes from the work in progress — observations, questions, ideas, experiments, and discoveries along the way.
Field notes
6 entries
Desk notes
Ideas & observations
Research log
Oct 06
2026
#001
Checking reads
bcftools query -i 'GT="AA"' \ -f '%CHROM\t%POS\t%REF\t%ALT[\t%AD]\n' sample.vcf.gz \ | awk -F'\t' '{split($5,a,","); af=a[2]/(a[1]+a[2]); if (af < 0.85) print $0 "\t" af}' This pri…
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Oct 06
2026
#002
Don't trust the GT field. Check the reads.
A VCF's genotype field (GT) is the caller's conclusion, not the evidence. I had two "homozygous" candidates collapse when I looked at the reads. One was called 1/1 even though 34% …
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Sep 08
2026
#003
Transcript annotation QC (KEEP IN MIND: damaging to which transcript?)
Never interpret a variants consequence from the annotation tool alone A single gene could potentially have multiple transcript due to alternative splicing. Before we interpret: Che…
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Aug 31
2026
#004
Why a frameshift doesnt always mean pathogenic
Ask, could translation reinitiation occur, or could the transcript undergo NMD? Positioning of the variant? could alternative splicing rescue the transcript? IMPORTANT: check gnomA…
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Aug 21
2026
#005
Franklin Genoox
Just as a Tip, uploading your VCF files into https://franklin.genoox.com/ Allows you to view the variants in a cleaner and easier way, especially if you have trio WES You can compa…
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Aug 21
2026
#006
001 - Purpose
Not everything I learn belongs in a paper. This notebook is a place for questions and thoughts I come up with while working with data and interesting variants. Learning things I do…
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Omar Abousaad · Research NotesKeep asking why.