NAME

       bwa-mem2_mem - Sequence alignment using Burrows-Wheeler Transform

SYNOPSIS

       bwa-mem2 mem [options] <idxbase> <in1.fq> [in2.fq]

DESCRIPTION

       Looking  to  launch  executable  "/build/bwa-mem2-idd0gu/bwa-mem2-2.2.1/./bwa-mem2.avx2",  simd  =  .avx2
       Launching               executable                "/build/bwa-mem2-idd0gu/bwa-mem2-2.2.1/./bwa-mem2.avx2"
       -----------------------------  Executing  in  AVX2 mode!!  ----------------------------- * SA compression
       enabled with xfactor: 8

OPTIONS

              Algorithm options:

       -o STR Output SAM file name

       -t INT number of threads [1]

       -k INT minimum seed length [19]

       -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

       -o     output file name missing

       -P     skip pairing; mate rescue performed unless -S also in use

   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]

   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)

       -5     for split alignment, take the alignment with the smallest coordinate as primary

       -q     don't modify mapQ of supplementary alignments

       -K INT process INT input bases in each batch regardless of nThreads (for reproducibility) []

       -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.

bwa-mem2 mem 2.2.1                                November 2021                                  BWA-MEM2_MEM(1)