How to Look Up Your Own Variants in NCBI dbSNP
A working guide to rsIDs: what they mean, how to annotate your own VCF against dbSNP, and how to handle merges and withdrawn records.
Tag: variants
6 posts
MTHFR rs1801131 (A1298C): reading it from your own data
What the A1298C variant is, how to pull it correctly out of a VCF or a consumer array file without getting burned by strand, and which blood measurements tell you more than the genotype does.
What Variant Effect Predictors Do, and Which Ones to Run on Your Own Genome
A working guide to variant effect predictors: what they score, how to run VEP with the right plugins, and which scores to trust.
Is Exome Sequencing Worth It, or Should You Just Sequence the Genome?
What whole exome sequencing covers, where capture fails, and how to check the quality of an exome you already own.
How to Read Your Own DNA Sequence From Raw Files
A practical walkthrough of going from FASTQ, BAM/CRAM, and VCF files to an actual nucleotide sequence you can read, translate, and check against the reads it came from.
VCF Annotation Tools: What to Run on Your Own Genome
A working pipeline for annotating a personal whole-genome VCF: normalize with bcftools, annotate with Ensembl VEP offline, join custom datasets with vcfanno or slivar, then filter down to something you can read.