Usage: bwa mem [options] <idxbase> <in1.fq> [in2.fq]

Algorithm options: -w INT band width for banded alignment [100] -d INT off-diagonal X-dropoff [100] -r FLOAT look for internal seeds inside a seed longer than {-k} * FLOAT [1.5] -y INT seed occurrence for the 3rd round seeding [20] -c INT skip seeds with more than INT occurrences [500] -D FLOAT drop chains shorter than FLOAT fraction of the longest overlapping chain [0.50] -W INT discard a chain if seeded bases shorter than INT [0] -m INT perform at most INT rounds of mate rescues for each read [50] -S skip mate rescue -P skip pairing; mate rescue performed unless -S also in use -e discard full-length exact matches

Scoring options:

-A INT score for a sequence match, which scales options -TdBOELU unless overridden [1] -B INT penalty for a mismatch [4] -O INT[,INT] gap open penalties for deletions and insertions [6,6] -E INT[,INT] gap extension penalty; a gap of size k cost '{-O} + {-E}*k' [1,1] -L INT[,INT] penalty for 5'- and 3'-end clipping [5,5] -U INT penalty for an unpaired read pair [17]

-x STR read type. Setting -x changes multiple parameters unless overriden [null] pacbio: -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0 (PacBio reads to ref) ont2d: -k14 -W20 -r10 -A1 -B1 -O1 -E1 -L0 (Oxford Nanopore 2D-reads to ref) intractg: -B9 -O16 -L5 (intra-species contigs to ref)

Input/output options:

-p smart pairing (ignoring in2.fq) -R STR read group header line such as '@RG\tID:foo\tSM:bar' [null] -H STR/FILE insert STR to header if it starts with @; or insert lines in FILE [null] -j treat ALT contigs as part of the primary assembly (i.e. ignore <idxbase>.alt file)

-v INT verbose level: 1=error, 2=warning, 3=message, 4+=debugging [3] -T INT minimum score to output [30] -h INT[,INT] if there are <INT hits with score >80% of the max score, output all in XA [5,200] -a output all alignments for SE or unpaired PE -C append FASTA/FASTQ comment to SAM output -V output the reference FASTA header in the XR tag -Y use soft clipping for supplementary alignments -M mark shorter split hits as secondary

-I FLOAT[,FLOAT[,INT[,INT]]] specify the mean, standard deviation (10% of the mean if absent), max (4 sigma from the mean if absent) and min of the insert size distribution. FR orientation only. [inferred]

Note: Please read the man page for detailed description of the command line and options.

GATK-RealignTargetCreator.cwl is developed for CWL consortium Prints all reads that have a mapping quality above zero Usage: java -Xmx4g -jar GenomeAnalysisTK.jar -T PrintReads -R reference.fasta -I input1.bam -I input2.bam -o output.bam --read_filter MappingQualityZero

GATK-RealignTargetCreator.cwl is developed for CWL consortium It accepts 3 input files and produces a file containing list of target intervals to pass to the IndelRealigner. Usage: java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R reference.fasta -I input.bam --known indels.vcf -o forIndelRealigner.intervals.

samtools-view.cwl is developed for CWL consortium Usage: samtools view [options] <in.bam>|<in.sam>|<in.cram> [region ...]

Options: -b output BAM -C output CRAM (requires -T) -1 use fast BAM compression (implies -b) -u uncompressed BAM output (implies -b) -h include header in SAM output -H print SAM header only (no alignments) -c print only the count of matching records -o FILE output file name [stdout] -U FILE output reads not selected by filters to FILE [null] -t FILE FILE listing reference names and lengths (see long help) [null] -T FILE reference sequence FASTA FILE [null] -L FILE only include reads overlapping this BED FILE [null] -r STR only include reads in read group STR [null] -R FILE only include reads with read group listed in FILE [null] -q INT only include reads with mapping quality >= INT [0] -l STR only include reads in library STR [null] -m INT only include reads with number of CIGAR operations consuming query sequence >= INT [0] -f INT only include reads with all bits set in INT set in FLAG [0] -F INT only include reads with none of the bits set in INT set in FLAG [0] -x STR read tag to strip (repeatable) [null] -B collapse the backward CIGAR operation -s FLOAT integer part sets seed of random number generator [0]; rest sets fraction of templates to subsample [no subsampling] -@ INT number of BAM compression threads [0]

GATK-RealignTargetCreator.cwl is developed for CWL consortium It performs local realignment of reads around indels. Usage: java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R reference.fasta -I input.bam --known indels.vcf -o forIndelRealigner.intervals.

Usage:

GATK-RealignTargetCreator.cwl is developed for CWL consortium Call germline SNPs and indels via local re-assembly of haplotypes

GATK-BaseRecalibrator.cwl is developed for CWL consortium It generate base recalibration table to compensate for systematic errors in basecalling confidences Usage: java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R reference.fasta -I my_reads.bam -knownSites latest_dbsnp.vcf -o recal_data.table.