{"id":6243,"projects":[69],"description":"Usage: bwa mem [options] <idxbase> <in1.fq> [in2.fq]\n\nAlgorithm options:\n       -w INT        band width for banded alignment [100]\n       -d INT        off-diagonal X-dropoff [100]\n       -r FLOAT      look for internal seeds inside a seed longer than {-k} * FLOAT [1.5]\n       -y INT        seed occurrence for the 3rd round seeding [20]\n       -c INT        skip seeds with more than INT occurrences [500]\n       -D FLOAT      drop chains shorter than FLOAT fraction of the longest overlapping chain [0.50]\n       -W INT        discard a chain if seeded bases shorter than INT [0]\n       -m INT        perform at most INT rounds of mate rescues for each read [50]\n       -S            skip mate rescue\n       -P            skip pairing; mate rescue performed unless -S also in use\n       -e            discard full-length exact matches\n\nScoring options:\n\n       -A INT        score for a sequence match, which scales options -TdBOELU unless overridden [1]\n       -B INT        penalty for a mismatch [4]\n       -O INT[,INT]  gap open penalties for deletions and insertions [6,6]\n       -E INT[,INT]  gap extension penalty; a gap of size k cost '{-O} + {-E}*k' [1,1]\n       -L INT[,INT]  penalty for 5'- and 3'-end clipping [5,5]\n       -U INT        penalty for an unpaired read pair [17]\n\n       -x STR        read type. Setting -x changes multiple parameters unless overriden [null]\n                     pacbio: -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0  (PacBio reads to ref)\n                     ont2d: -k14 -W20 -r10 -A1 -B1 -O1 -E1 -L0  (Oxford Nanopore 2D-reads to ref)\n                     intractg: -B9 -O16 -L5  (intra-species contigs to ref)\n\nInput/output options:\n\n       -p            smart pairing (ignoring in2.fq)\n       -R STR        read group header line such as '@RG\\tID:foo\\tSM:bar' [null]\n       -H STR/FILE   insert STR to header if it starts with @; or insert lines in FILE [null]\n       -j            treat ALT contigs as part of the primary assembly (i.e. ignore <idxbase>.alt file)\n\n       -v INT        verbose level: 1=error, 2=warning, 3=message, 4+=debugging [3]\n       -T INT        minimum score to output [30]\n       -h INT[,INT]  if there are <INT hits with score >80% of the max score, output all in XA [5,200]\n       -a            output all alignments for SE or unpaired PE\n       -C            append FASTA/FASTQ comment to SAM output\n       -V            output the reference FASTA header in the XR tag\n       -Y            use soft clipping for supplementary alignments\n       -M            mark shorter split hits as secondary\n\n       -I FLOAT[,FLOAT[,INT[,INT]]]\n                     specify the mean, standard deviation (10% of the mean if absent), max\n                     (4 sigma from the mean if absent) and min of the insert size distribution.\n                     FR orientation only. [inferred]\n\nNote: Please read the man page for detailed description of the command line and options.","image":"","tags":"","type":"","title":"dockstore-tool-bwa-mem","url":"https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fcollaboratory%2Fdockstore-tool-bwa-mem","authors":[1],"rubrics":[25]}