Sequences Alignment and Sorting by Coordinate

We automatically retrieve BAM filenames based on the FASTA_R1 port name We assume FASTA_R1 name to be SAMPLENAME.R1.FASTQ or SAMPLENAME.R1.fastq.gz

Alignment via Burrows-Wheeler transformation using BWA-MEM algorithm

Sorts the input SAM or BAM

Post Alignment File Processing

We automatically retrieve BAM filenames based on the FASTA_R1 port name We assume FASTA_R1 name to be SAMPLENAME.R1.FASTQ or SAMPLENAME.R1.fastq.gz

MarkDuplicates examines aligned records in the supplied SAM or BAM file to locate duplicate molecules. All records are then written to the output file with the duplicate records flagged

Here we retreave sequencing information from the FASTA port Notice that the parameters RGPL and RGLB may be adjusted according to your biological experiment and sequencing platform

AddOrReplaceReadGroups replaces all read groups in the INPUT file with a single new read group and assigns all reads to this read group in the OUTPUT BAM

BuildBamIndex generates a BAM index (.bai) file

ValidateSamFile read a SAM or BAM file and report on its validity.

Genome Analysis Toolkit

We automatically retrieve BAM filenames based on the FASTA_R1 port name We assume FASTA_R1 name to be SAMPLENAME.R1.FASTQ or SAMPLENAME.R1.fastq.gz

BuildBamIndex generates a BAM index (.bai) file.

RealignerTargetCreator defines intervals to target for local realignment

IndelRealigner aplies the realignment in the targets from RealignerTargetCreator

BaseRecalibrator generates base recalibration table to compensate for systematic errors in basecalling confidences

PrintReads writes out sequence read data (for filtering, merging, subsetting etc)

HaplotypeCaller calls germline SNPs and indels via local re-assembly of haplotypes