cellme

Convert a human cell line identifier into a truth-track VCF of its known mutations.

Introduction

cellme builds a truth/known VCF for a cell line by resolving a name such as MOLT-4 to a Cancer Cell Line Encyclopedia sample, fetching that sample's somatic mutations from the cBioPortal REST API, and writing them as a sorted VCF. The mutation source is the ccle_broad_2019 study. CCLE reports its coordinates against hg19 (GRCh37); by default cellme lifts them to hg38 (GRCh38), and --build hg19 keeps the native coordinates.

Installation

Install the release from PyPI with pip:

pip install cellme

Usage

Write an hg38 truth track for the cell line MOLT-4 to a file:

cellme "MOLT-4" --build hg38 --reference /ref/hg38.fa --output MOLT-4.hg38.vcf.gz

Important

Always pass --reference with a FASTA for the build you target, as shown above. It ensures the correct anchor bases are set for insertions and deletions. Without it, indel anchor bases fall back to a placeholder N and those records are marked ANCHOR=placeholder.

The build keys are hg38 and hg19 (the Ensembl names GRCh38 and GRCh37 are accepted as aliases). The query is matched case-insensitively on the leading cell line token, so MOLT-4, MOLT4, and the full MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE sample ID all resolve to the same sample.

VCF INFO Fields

Every record is annotated with compact, self-describing INFO fields.

Key	Type	Description
GENE	String	HUGO gene symbol.
PROTEIN_CHANGE	String	Protein-level change in CCLE short form (HGVS p.-like), e.g. R306*.
VARIANT_CLASS	String	Variant classification (MAF-style), e.g. Missense_Mutation.
VARIANT_TYPE	String	Sequence alteration type reported by CCLE: SNP, DNP, INS, or DEL.
CELL_LINE	String	Cell line resolved from the query.
SAMPLE_ID	String	CCLE sample identifier for the cell line.
ENTREZ	Integer	NCBI Entrez gene identifier.
REFSEQ	String	RefSeq mRNA accession for the annotated transcript.
PROTEIN_POS	String	Affected protein position or range, 1-based.
SOURCE	String	Source database and study, e.g. cBioPortal CCLE ccle_broad_2019.
ORIGINAL_BUILD	String	Genome build of the source coordinates before any liftover.
ORIGINAL_LOCUS	String	Original locus before liftover in UCSC position format, e.g. chr17:7577022.
LIFTED	Flag	Coordinate was lifted from ORIGINAL_BUILD to the output reference build.
ANCHOR	String	Provenance of the indel anchor base: reference or placeholder.

The ID column is set to a stable gene:proteinChange token where one is available, for example TP53:R306*, and falls back to gene:chrom:pos otherwise.

Development and Testing

See the contributing guide for more information.