This workflow is for pre-processing of SG10K samples (shallow human WGS) which are meant to be further processed with gotcloud. The following steps are performed:
- Alignment of reads with BWA-MEM against hs37d5 from the gotcloud bundle
- Duplicate marking with samblaster
- Base-quality recalibration with bamutils' recab. See
{sample}.bwamem.fixmate.mdups.srt.recal.bam - Creation of simple mapping statistics (bamstats, idxstats). See
{sample}.bwamem.fixmate.mdups.srt.recal.bamstats - Contamination check with verifyBamID (Chinese, Indian and Malay
vcf's). See
{sample}.bwamem.fixmate.mdups.srt.recal.{race}.selfSM
These and following steps are prone to change and should hence not considered as production version!