NAME

       snap-aligner_index - scalable nucleotide alignment program

SYNOPSIS

       snap-aligner index <input.fa> <output-dir> [<options>]

DESCRIPTION

       Welcome to SNAP version 2.0.3.

OPTIONS

       -s     Seed size (default: 24)

       -h     Hash table slack (default: 0.3)

       -t     Specify  the  maximum  number of threads to use. Default is the number of cores. Do
              not leave a space after the -t, e.g., -t16

       -B<chars>
              Specify characters to use as chromosome name terminators in the FASTA header  line;
              these  characters and anything after are not part of the chromosome name.  You must
              specify all characters on a single -B switch.  So,  for  example,  with  -B_|,  the
              FASTA  header  line  '>chr1|Chromosome 1' would generate a chromosome named 'chr1'.
              There's a separate flag for indicating that a space is a terminator.

       -bSpace
              Indicates that the space and tab characters are terminators  for  chromosome  names
              (see -B above).  This may be used in addition to other terminators specified by -B.
              -B and -bSpace are case sensitive.  This is the default.

       -bSpace-
              Indicates that space and tab characters should be included in chromosome names.

       -p     Specify the number of Ns to put as padding between chromosomes.  This  must  be  as
              large  as  the  largest  edit  distance  you'll ever use, and there's a performance
              advantage to have it be  bigger  than  any  read  you'll  process  or  gap  between
              paired-end  reads.   Default is 2000.  Specify the amount of padding directly after
              -p without a space.

       -H     Build a histogram of seed popularity.  This is just for information, it's not  used
              by  SNAP.   Specify  the  histogram  file  name directly after -H without leaving a
              space.

       -exact Compute hash table sizes exactly.  This will slow down  index  build,  but  usually
              will result in smaller indices.

       -keysize
              The  number  of bytes to use for the hash table key.  Larger values increase SNAP's
              memory footprint, but allow larger seeds.  By default it's  autoselected  based  on
              the seed size.

       -large Build   a  larger  index  that's  a  little  faster,  particularly  for  runs  with
              quick/inaccurate parameters.  Increases index size by about 30%, depending  on  the
              other index parameters and the contents of the reference genome

       -locationSize
              The  size  of  the  genome  locations stored in the index.  This can be from 4 to 8
              bytes.  The locations need to be big enough not only to index the genome, but  also
              to  allow  some  space  for  representing seeds that occur multiple times.  For the
              human genome, it will fit with four byte locations  if  the  seed  size  is  20  or
              larger,  but  needs 5 (or more) for smaller seeds.  Making the location size bigger
              than necessary will just waste (lots of) space, so unless  you're  doing  something
              quite  unusual,  the  right  answer is 4 or 5.  Default is based on seed size: 4 if
              it's 20 or greater, 5 otherwise.

       -sm    Use a temp file to work better in smaller memory.  This only helps  a  little,  but
              can be the difference if you're close.  In particular, this will generally use less
              memory than the index will use once it's built, so if this doesn't work  you  won't
              be  able to use the index anyway. However, if you've got sufficient memory to begin
              with, this option will just slow down the index build by doing extra, useless IO.

       -AutoAlt-
              Don't automatically mark ALT contigs.  Otherwise, any contig  whose  name  ends  in
              '_alt'  (regardless  of  captialization)  or  starts  with HLA- will be marked ALT.
              Others will not.

       -maxAltContigSize Specify a size at or below which all contigs  are  automatically  marked
              ALT, unless overridden by name using the args below

       -altContigName
              Specify  the  (case  independent)  name of an alt to mark a contig.  You can supply
              this parameter as often as you'd like

       -altContigFile
              Specify the name of a file with a list of alt contig names, one per line.  You  may
              specify this as often as you'd like

       -nonAltContigName Specify the name of a contig that's not an alt, regardless of its size

       -nonAltContigFile  Specify  the  name  of  a file that contains a list of contigs (one per
              line) that will not be marked ALT regardless of size

       -altLiftoverFile
              Specify the file containing ALT-to-REF mappings (SAM format).  e.g.,  hs38DH.fa.alt
              from bwa-kit

       -q     Quiet  mode:  don't  print status messages (other than the welcome message which is
              printed prior to parsing args).  Error messages are still printed.

       -qq    Super quiet mode: don't print status or error messages