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Small Variant input files

Gene input file

  • parameter: --gene_input
  • default: ${projectDir}/input/gene_list.txt

A text file with no header, that includes a one-per-line list of genes (HGNC symbols or Ensembl IDs).

genes.txt 
BRCA1
ENSG00000227518
TNF

Info

  1. The maximum number of genes per query is ten. If you need to query more than ten genes, please run the workflow with multiple smaller gene sets. For a large set of genes, consider using aggV2 (see aggV2 Code Book::Functional Annotation Queries).
  2. Query genes in the input list that are not found in BioMart reference data are written to <build>_genes_not_found.txt.

Samplesheet file

  • parameter: --samplesheet
  • default: null
  • by default, i.e., if no samplesheet file is provided, a LabKey query is run to select 1000KGP rare disease and cancer germline participants for both GRCh37 and GRCh38

A comma-separated value (CSV) file with a header, and columns: participant_id, platekey, genome_build, file_path, delivery_version, file_sub_type, type

samplesheet.csv 
participant_id,platekey,genome_build,file_path,delivery_version,file_sub_type,type
SAMPLE2,PLATEKEY2,GRCh37,s3://path_to_sample_file/SAMPLE2_GRCh37.vcf.gz,V4,Standard VCF,rare disease germline
SAMPLE2,PLATEKEY2,GRCh38,s3://path_to_sample_file/SAMPLE2_GRCh38.vcf.gz,V4,Standard VCF,rare disease germline
SAMPLE3,PLATEKEY3,GRCh37,s3://path_to_sample_file/SAMPLE3_GRCh37.vcf.gz,V4,Standard VCF,rare disease germline
SAMPLE3,PLATEKEY3,GRCh38,s3://path_to_sample_file/SAMPLE3_GRCh38.vcf.gz,V4,Standard VCF,rare disease germline
SAMPLE4,PLATEKEY4,GRCh37,s3://path_to_sample_file/SAMPLE4_GRCh37.vcf.gz,V4,Standard VCF,rare disease germline
SAMPLE4,PLATEKEY4,GRCh38,s3://path_to_sample_file/SAMPLE4_GRCh38.vcf.gz,V4,Standard VCF,rare disease germline
SAMPLE5,PLATEKEY5,GRCh37,s3://path_to_sample_file/SAMPLE5_GRCh37.vcf.gz,V4,Standard VCF,rare disease germline
SAMPLE5,PLATEKEY5,GRCh38,s3://path_to_sample_file/SAMPLE5_GRCh38.vcf.gz,V4,Standard VCF,rare disease germline
SAMPLE6,PLATEKEY6,GRCh37,s3://path_to_sample_file/SAMPLE6_GRCh37.vcf.gz,V4,Standard VCF,rare disease germline
SAMPLE6,PLATEKEY6,GRCh38,s3://path_to_sample_file/SAMPLE6_GRCh38.vcf.gz,V4,Standard VCF,rare disease germline
SAMPLE7,PLATEKEY7,GRCh37,s3://path_to_sample_file/SAMPLE7_GRCh37.vcf.gz,V4,Standard VCF,rare disease germline
SAMPLE7,PLATEKEY7,GRCh38,s3://path_to_sample_file/SAMPLE7_GRCh38.vcf.gz,V4,Standard VCF,rare disease germline

Samplesheet considerations

  • use the latest GEL data release
  • use a minimum sample size of four particpants (for each genome build included)
  • use the latest delivery_date
  • use either delivery_version Illumina (V2 and/or V4), or Dragen (Dragen_Pipeline2.0)
  • use only germline genomes

For reference, below is the default SQL query made to LabKey on HPC

LabKey query 
SELECT
    g.participant_id,
    g.platekey,
    g.genome_build,
    g.file_path
FROM
    genome_file_paths_and_types AS g
INNER JOIN
    participant AS p ON p.participant_id = g.participant_id
WHERE type IN ('rare disease germline', 'cancer germline')
AND g.participant_id NOT IN ({','.join(excluded_participants)})
AND genome_build = '{genome_build}'
AND file_sub_type = 'Standard VCF'
AND normalised_consent_form != 'cohort-tracerx'
AND g.delivery_version != 'Dragen_Pipeline2.0'
AND NOT EXISTS (
    SELECT 1 FROM genome_file_paths_and_types AS g_newer
    WHERE g_newer.participant_id = g.participant_id
    AND g_newer.type = g.type
    AND g_newer.genome_build = g.genome_build
    AND g_newer.file_sub_type = g.file_sub_type
    AND g_newer.delivery_date > g.delivery_date
    AND g_newer.delivery_version != 'Dragen_Pipeline2.0'