Tapestri Pipeline

This pipeline processes single-cell DNA-seq data generated with the Mission Bio Tapestri Genomics Platform.

Input Files:

  • Seq run 1 Fastq.gz files generated from an Illumina MiSeq/Hiseq instrument
  • Panel BED file in zipped format provides user-defined set of targeted positions
  • [OPTIONAL] Seq run 2 Fastq.gz files generated from a second Illumina MiSeq/Hiseq instrument on the same libraries as Seq run 1.
  • [OPTIONAL] White list BED file. The chromosomal positions in this white list will be reported even if they do not contain a mutation

 

Primary output files:

  • loom file is used for Tapestri Insights
  • vcf.gz is a compressed VCF file generated by GATK
  • report file summarizes metrics in PDF format