This pipeline calls somatic variants with LoFreq Somatic.
The following steps are performed:
- Read mapping (see
cfg/references.yamlfor references used by default and also refer to option--references-cfg) - Duplicate marking with samblaster (if not instructed otherwise)
- Realignment with
lofreq viterbi - Base quality recalibration with
Lacer(Swaine Chen <mailto:[email protected]>), unless sequencing type is "targeted" - Calling of variants (SNVs and indels) with LoFreq
- Recalibrated BAM file per sample:
{sample}.bwamem.lofreq.lacer.bam - Called variants:
{sample}.bwamem.lofreq.lacer.{type}.vcf.gz(annotated:{sample}.bwamem.lofreq.lacer.{type}.snpeff.vcf.gz) - Mapping statistics:
{sample}.bwamem.lofreq.lacer.bamstats