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
--referencewith 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 placeholderNand those records are markedANCHOR=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.
1 maintainer
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