pipelines-docs

Long-Read Variant Calling

The pipeline detects candidate single-nucleotide variants (SNVs) from long-read sequencing data using longcallD. PacBio HiFi data is processed when available to complement variants detected from short-read sequencing.

All sequencing libraries associated with a tissue sample are merged prior to variant calling and processed jointly.

longcallD Variant Calling

Run longcallD

longcallD call -s \
  -n sample \
  --hifi \
  -o output.vcf \
  -T mei_reference.fasta \
  reference.fasta \
  sample.cram

Arguments:

• -s: call low-allele-fraction somatic/mosaic variants.
• --hifi: use the PacBio HiFi sequencing model.

Mobile Element Insertion Reference

longcallD requires an additional reference FASTA (-T) used to detect mobile element insertions (MEI). For additional details and to download the MEI reference file (AluY_L1_SVA_cons_noPA.fa), please refer to the developer repository here.

Multiple Input Files

The pipeline supports the inclusion of multiple CRAM files during variant calling. Additional CRAM files can be provided using the -X option and are processed jointly with the primary CRAM during variant calling.

Software Version

The pipeline uses longcallD version 0.0.8.

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