CRAM Subsetting¶

Subset CRAM to Genomic Region¶

Extract reads from a specific genomic region to create a smaller, focused CRAM file.

Python API Documentation¶

grid.utils.subset_cram¶

grid.utils.subset_cram.subset_cram(cram_path, region, output_path, reference=None)¶

Subset a CRAM file for a specific genomic region.

Parameters:

cram_path (str) – Input CRAM file.
region (str) – Region in ‘chr:start-end’ format (e.g., ‘chr6:160000000-160100000’).
output_path (str) – Path to output CRAM file.
reference (str) – Reference genome FASTA (required for CRAM output)

Returns:

Path to the subset CRAM file.

Return type:

str

Usage¶

Via CLI¶

# Using region string
grid subset \
    --cram input.cram \
    --region chr6:160000000-160100000 \
    --output subset.cram \
    --reference refs/hs37d5.fa

# Using separate coordinates
grid subset \
    --cram input.cram \
    --chrom chr6 \
    --start 160000000 \
    --end 160100000 \
    --output subset.cram \
    --reference refs/hs37d5.fa

Via Python¶

from grid.utils.subset_cram import subset_cram

subset_path = subset_cram(
    cram_path="input.cram",
    region="chr6:160000000-160100000",
    output_path="subset.cram",
    reference="refs/hs37d5.fa"
)

Description¶

This utility extracts reads overlapping a specific genomic region:

Uses samtools view to extract region
Maintains CRAM format and compression
Creates index (.crai) for output file
Preserves header information

Use cases:

Testing - Work with smaller files during development
Sharing - Extract specific regions for collaboration
Performance - Faster processing on region of interest
Storage - Reduce file sizes for targeted analysis

Region Format¶

Regions can be specified as:

Full format: chr6:160000000-160100000
Chromosome only: chr6 (entire chromosome)
No end: chr6:160000000 (from position to end)

Coordinates are 0-based, following SAM/BAM conventions.

Dependencies¶

samtools - Must be installed and in PATH
pysam - Python library for BAM/CRAM handling

Output¶

Creates two files:

<output>.cram - Subset CRAM file
<output>.cram.crai - Index for subset CRAM