Aligning Your Whole-Genome FASTQs with BWA-MEM
A step-by-step guide to indexing a human reference, running bwa mem on 30x whole-genome FASTQs, and producing a sorted CRAM for variant calling.
Tag: samtools
3 posts
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.
How to Use WGS Extract, and When to Use samtools Instead
A working guide to verifying, converting and analyzing a personal 30x whole-genome file. Covers the reference build, CRAM to BAM and coverage QC.