---
title: Supported File Formats
---

# Supported File Formats [NEEDS CURATION]

ZaroPGx supports multiple genomic data formats with automatic conversion and processing.

## Variant Call Format (VCF)
VCF is the standard format for storing genetic variant information. ZaroPGx can process VCF 4.x files directly without preprocessing.

### Processing Path
```
VCF → Header Analysis → PyPGx → PharmCAT → Reports
```

## Binary Alignment Map (BAM)
BAM files contain aligned sequencing reads and are commonly used for variant calling and analysis.

### Processing Path
```
BAM → HLA Typing → PyPGx → PharmCAT → Reports
```

## Compressed BAM (CRAM)
CRAM is a compressed version of BAM that uses reference-based compression for smaller file sizes.

### Processing Path
```
CRAM → GATK (BAM conversion) → HLA Typing → PyPGx → PharmCAT → Reports
```

## Sequence Alignment Map (SAM)
SAM is the text-based format for aligned sequences, often used as an intermediate format.

### Processing Path
```
SAM → GATK (BAM conversion) → HLA Typing → PyPGx → PharmCAT → Reports
```

## FASTQ Format
FASTQ files contain raw sequencing reads with quality scores and are the starting point for most genomic analyses.

### Processing Path
```
FASTQ → HLA Typing → GATK (BAM generation) → PyPGx → PharmCAT → Reports
```

## Reference Genome Support
- **GRCh38/hg38** (Recommended)
- **GRCh37/hg19** (Legacy)

## File Size Considerations

### Typical File Sizes
| Format | Whole Genome | Exome | Targeted Panel |
|--------|--------------|-------|----------------|
| **VCF** | 1-5 GB | 50-200 MB | 1-10 MB |
| **BAM** | 50-100 GB | 2-5 GB | 50-500 MB |
| **CRAM** | 15-30 GB | 500 MB-1 GB | 10-100 MB |
| **FASTQ** | 100-200 GB | 5-10 GB | 100 MB-1 GB |


## Next Steps

- **Learn about usage**: {doc}`usage`
- **Understand reports**: {doc}`reports`
- **Configure processing**: {doc}`../advanced-configuration`
- **Troubleshoot issues**: {doc}`troubleshooting`