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