DESCRIPTION

Welcome to SNAP version 1.0beta.18.

Too few parameters Usage: snap-aligner paired <index-dir> <inputFile(s)> [<options>] where <input file(s)> is a list of files to process.

OPTIONS

-o

filename output alignments to filename in SAM or BAM format, depending on the file extension or explicit type specifier (see below). Use a dash with an explicit type specifier to write to stdout, so for example -o -sam - would write SAM output to stdout

-d

maximum edit distance allowed per read or pair (default: 15)

-n

number of seeds to use per read

-sc

Seed coverage (i.e., readSize/seedSize). Floating point. Exclusive with -n. (default uses -n)

-h

maximum hits to consider per seed (default: 300)

-ms

minimum seed matches per location (default: 1)

-t

number of threads (default is one per core)

-b

bind each thread to its processor (this is the default)

--b

Don't bind each thread to its processor (note the double dash)

-P

disables cache prefetching in the genome; may be helpful for machines with small caches or lots of cores/cache

-so

sort output file by alignment location

-sm

memory to use for sorting in Gb

-x

explore some hits of overly popular seeds (useful for filtering)

-f

stop on first match within edit distance limit (filtering mode)

-F

filter output (a=aligned only, s=single hit only (MAPQ >= 10), u=unaligned only, l=long enough to align (see -mrl))

-S

suppress additional processing (sorted BAM output only) i=index, d=duplicate marking

-I

ignore IDs that don't match in the paired-end aligner

-Cxx must be followed by two + or - symbols saying whether to clip low-quality

bases from front and back of read respectively; default: back only (-C-+)

-M

indicates that CIGAR strings in the generated SAM file should use M (alignment match) rather than = and X (sequence (mis-)match). This is the default

-=

use the new style CIGAR strings with = and X rather than M. The opposite of -M

-G

specify a gap penalty to use when generating CIGAR strings

-pf

specify the name of a file to contain the run speed

--hp Indicates not to use huge pages (this may speed up index load and slow down alignment)

This is the default

-hp

Indicates to use huge pages (this may speed up alignment and slow down index load).

-D

Specifies the extra search depth (the edit distance beyond the best hit that SNAP uses to compute MAPQ). Default 2

-rg

Specify the default read group if it is not specified in the input file

-R

Specify the entire read group line for the SAM/BAM output. This must include an ID tag. If it doesn't start with '@RG' SNAP will add that. Specify tabs by \t. Two backslashes will generate a single backslash. backslash followed by anything else is illegal. So, '-R @RG\tID:foo\tDS:my data' would generate reads with default tag foo, and an @RG line that also included the DS:my data field.

-sa

Include reads from SAM or BAM files with the secondary (0x100) or supplementary (0x800) flag set; default is to drop them.

-om

Output multiple alignments. Takes as a parameter the maximum extra edit distance relative to the best alignment to allow for secondary alignments

-omax Limit the number of alignments per read generated by -om.

This means that if -om would generate more

than -omax secondary alignments, SNAP will write out only the best -omax of them, where 'best' means 'with the lowest edit distance'. Ties are broken arbitrarily.

-mpc Limit the number of alignments generated by -om to this many per contig (chromosome/FASTA entry);

'mpc' means 'max per contig; default unlimited.

This filter is applied prior to -omax. The primary alignment

is counted.

-pc

Preserve the soft clipping for reads coming from SAM or BAM files

-xf

Increase expansion factor for BAM and GZ files (default 1.0)

-hdp Use Hadoop-style prefixes (reporter:status:...) on error messages, and emit hadoop-style progress messages

-mrl Specify the minimum read length to align, reads shorter than this (after clipping) stay unaligned.

This should be

a good bit bigger than the seed length or you might get some questionable alignments.

Default 50

-map Use file mapping to load the index rather than reading it.

This might speed up index loading in cases

where SNAP is run repatedly on the same index, and the index is larger than half of the memory size of the machine. On some operating systems, loading an index with -map is much slower than without if the index is not in memory. You might consider adding -pre to prefetch the index into system cache when loading with -map when you don't expect the index to be in cache.

-pre Prefetch the index into system cache.

This is only meaningful with -map, and only helps if the index is not

already in memory and your operating system is slow at reading mapped files (i.e., some versions of Linux, but not Windows).

-lp

Run SNAP at low scheduling priority (Only implemented on Windows)

-nu

No Ukkonen: don't reduce edit distance search based on prior candidates. This option is purely for evaluating the performance effect of using Ukkonen's algorithm rather than Smith-Waterman, and specifying it will slow down execution without improving the alignments.

-no

No Ordering: don't order the evalutation of reads so as to select more likely candidates first. This option is purely for evaluating the performance effect of the read evaluation order, and specifying it will slow down execution without improving alignments.

-nt

Don't truncate searches based on missed seed hits. This option is purely for evaluating the performance effect of candidate truncation, and specifying it will slow down execution without improving alignments.

-wbs

Write buffer size in megabytes. Don't specify this unless you've gotten an error message saying to make it bigger. Default 16.

You may process more than one alignment without restarting SNAP, and if possible without reloading the index. In order to do this, list on the command line all of the parameters for the first alignment, followed by a comma (separated by a space from the other parameters) followed by the parameters for the next alignment (including single or paired). You may have as many of these as you please. If two consecutive alignments use the same index, it will not be reloaded. So, for example, you could do 'snap-aligner single hg19-20 foo.fq -o foo.sam , paired hg19-20 end1.fq end2.fq -o paired.sam' and it would not reload the index between the single and paired alignments. When specifying an input or output file, you can simply list the filename, in which case SNAP will infer the type of the file from the file extension (.sam or .bam for example), or you can explicitly specify the file type by preceding the filename with one of the

following type specifiers (which are case sensitive):

-fastq

-compressedFastq

-sam

-bam

-pairedFastq

-pairedInterleavedFastq

-pairedCompressedInterleavedFastq

So, for example, you could specify -bam input.file to make SNAP treat input.file as a BAM file, even though it would ordinarily assume a FASTQ file for input or a SAM file for output when it doesn't recoginize the file extension. In order to use a file name that begins with a '-' and not have SNAP treat it as a switch, you must explicitly specify the type. But really, that's just confusing and you shouldn't do it. Input and output may also be from/to stdin/stdout. To do that, use a - for the input or output file name and give an explicit type specifier. So, for example, snap-aligner aligner single myIndex -fastq - -o -sam - would read FASTQ from stdin and write SAM to stdout.

-s

min and max spacing to allow between paired ends (default: 50 1000).

-fs

force spacing to lie between min and max.

-H

max hits for intersecting aligner (default: 2000).

-mcp specifies the maximum candidate pool size (An internal data structure.

Only increase this if you get an error message saying to do so. If you're running out of memory, you may want to reduce it. Default: 1000000)

-F b additional option to -F to require both mates to satisfy filter (default is just one)

If you specify -F b together with one of the other -F options, -F b MUST be second

-ku

Keep unpaired-looking reads in SAM/BAM input. Ordinarily, if a read doesn't specify mate information (RNEXT field is * and/or PNEXT is 0) then the code that matches reads will immdeiately discard it. Specifying this flag may cause large memory usage for some input files, but may be necessary for some strangely formatted input files. You'll also need to specify this flag for SAM/BAM files that were aligned by a single-end aligner.