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lacer-lofreq

This pipeline calls somatic variants with LoFreq.

The following steps are performed:

  • Read mapping (see cfg/references.yaml for 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:slchen@gis.a-star.edu.sg>), unless sequencing type is "targeted"
  • Calling of somatic variants (SNVs and indels) with LoFreq Somatic

Summary

This pipeline maps your reads to a given reference, marks duplicate reads (if not instructed otherwise), realigns your reads with lofreq viterbi, recalibrates base qualities with Lacer (author: Swaine Chen <mailto:slchen@gis.a-star.edu.sg>) and calls SNVs and indels with LoFreq <http://csb5.github.io/lofreq/>.

Output

  • Realigned and recalibrated BAM file: {sample}.bwamem.lofreq.dedup.lacer.bam (dedup will be missing if mark duplicates was switched off)
  • Variants (snps or indels): BAM name + .{vartype}.vcf.gz
  • Variants annotated with SnpEff end in .{vartype}.snpeff.vcf.gz