Pipeline Steps

1. convert-BAM2FASTQ

Optional: Only run when BAM or CRAM are provided as input and realignment is not overriden.

Aligned data is back-converted to FASTQ using pipeline-convert-BAM2FASTQ.

2. align-DNA

FASTQ data is (re)aligned to the genome on a per-sample basis using pipeline-align-DNA.

3. calculate-targeted-coverage

For targeted or exome sequencing, depth for the target regions is assessed along with off-target coverage enrichment using pipeline-calculate-targeted-coverage.

4. recalibrate-BAM

The aligned BAM undergoes INDEL realignment and base quality score recalibration using pipeline-recalibrate-BAM.

5. generate-SQC-BAM

Quality control is performed on the recalibrated BAM using pipeline-generate-SQC-BAM.

6. call-gSNP

Germline SNPs are called using pipeline-call-gSNP.

7. call-sSNV

Somatic SNVs are called using pipeline-call-sSNV.

8. call-mtSNV

Mitochondrial SNVs are called using pipeline-call-mtSNV.

9. call-gSV

Germline SVs are called using pipeline-call-gSV.

10. call-sSV

Somatic SVs are called using pipeline-call-sSV.

11. call-sCNA

Somatic CNAs are called using pipeline-call-sCNA.

12. call-SRC

Subclonal reconstruction is performed using pipeline-call-SRC.