NGS & File Formats: Essential Concepts

If you're working with Next-Generation Sequencing (NGS) data, understanding file formats is key to managing your data efficiently. Here’s a quick overview:

• FASTQ — Raw sequencing reads with quality scores.
• SAM/BAM — Aligned reads; BAM is the compressed binary version of SAM (smaller + faster).
• CRAM — Like BAM but with better compression; great for large-scale projects.
• VCF — Variant Call Format; stores SNPs, indels, and structural variants.

Conversions Between Formats

samtools view -Sb file.sam > file.bam
samtools view -h file.bam > file.sam
samtools view -C -T reference.fasta file.bam > file.cram
samtools view -b -T reference.fasta file.cram > file.bam

Indexing Large Genomic Files

samtools index file.bam
samtools index file.cram
tabix -p vcf file.vcf.gz

Compression Comparison

CRAM < BAM < FASTQ.GZ (in terms of disk space saved).

CRAM is ideal for archiving; BAM balances speed and size; FASTQ.GZ stores raw reads but takes more space.

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