Genomic File Formats, 1000 genomes project
UZH BIO392 HS22 - Day 04
Izaskun Mallona (email: izaskun.mallona at sib.swiss).
Morning (on site, 9 am)
We will have a lecture and run a set of exercises (on site).
- Overview of the standard genomics data formats
- Basic file processing for bioinformatics
- wc, grep, awk
Afternoon (on site or online)
Exercises and project.
- SAM v1 format specification
- BEDtools paper
- 0-start, 1-start, open, closed: how do we count
- GFF3 format
- VCF format
Exercises 1-28 cover FASTA, FASTQ, SAM, BED, GTF and VCF. They include a small project.