.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.1.
.TH SNP_STORE "1" "September 2014" "snp_store 1.4.1+dfsg" "User Commands"
.SH NAME
snp_store \- SnpStore
.PP
SYNOPSIS
.IP
snp_store [OPTIONS] "GENOME FILE" "MAPPED READ FILE(S)"
.PP
DESCRIPTION
.IP
SNP and Indel Calling in Mapped Read Data.
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
Displays this help message.
.HP
\fB\-\-version\fR
.IP
Display version information
.IP
Options: :
.HP
\fB\-o\fR, \fB\-\-output\fR FILE
.IP
Output file for SNPs (must be set, no default construction).
.HP
\fB\-if\fR, \fB\-\-input\-format\fR NUM
.IP
Set input format: 0 for GFF format and 1 for SAM format (both must
be sorted according to genome positions). Default: 0.
.HP
\fB\-of\fR, \fB\-\-output\-format\fR NUM
.IP
Set output format: 0 to output all candidate snps amd 1 to output
successful candidate snps only. Default: 0.
.HP
\fB\-dc\fR, \fB\-\-dont\-clip\fR
.IP
Ignore clip tags in gff. Default: off.
.HP
\fB\-mu\fR, \fB\-\-multi\fR
.IP
Keep non\-unique fragmentStore.alignedReadStore. Default: off.
.HP
\fB\-hq\fR, \fB\-\-hide\-qualities\fR
.IP
Only show coverage (no qualities) in SNP output file. Default: off.
.HP
\fB\-sqo\fR, \fB\-\-solexa\-qual\-offset\fR
.IP
Base qualities are encoded as Ascii value \- 64 (instead of Ascii \-
33).
.HP
\fB\-id\fR, \fB\-\-indel\-file\fR FILE
.IP
Output file for called indels in gff format. Default: off.
.HP
\fB\-m\fR, \fB\-\-method\fR NUM
.IP
Set method used for SNP calling: 0 for threshold method and 1 for
maq method. Default: 1.
.HP
\fB\-mp\fR, \fB\-\-max\-pile\fR NUM
.IP
Maximal number of matches allowed to pile up at the same genome
position.
.HP
\fB\-mmp\fR, \fB\-\-merged\-max\-pile\fR
.IP
Do pile up correction on merged lanes. Default: off.
.HP
\fB\-mc\fR, \fB\-\-min\-coverage\fR NUM
.IP
Minimal required number of reads covering a candidate position.
.HP
\fB\-fc\fR, \fB\-\-force\-call\fR NUM
.IP
Always call base if count is >= fc, ignore other parameters.
Default: off. In range [1..inf].
.HP
\fB\-oa\fR, \fB\-\-orientation\-aware\fR
.IP
Distinguish between forward and reverse reads. Default: off.
.HP
\fB\-mpr\fR, \fB\-\-max\-polymer\-run\fR NUM
.IP
Discard indels in homopolymer runs longer than mpr.
.HP
\fB\-dp\fR, \fB\-\-diff\-pos\fR NUM
.IP
Minimal number of different read positions supporting the mutation.
.HP
\fB\-eb\fR, \fB\-\-exclude\-border\fR NUM
.IP
Exclude read positions within eb base pairs of read borders for SNV
calling.
.HP
\fB\-su\fR, \fB\-\-suboptimal\fR
.IP
Keep suboptimal reads.
.HP
\fB\-re\fR, \fB\-\-realign\fR
.IP
Realign reads around indel candidates.
.HP
\fB\-pws\fR, \fB\-\-parse\-window\-size\fR NUM
.IP
Genomic window size for parsing reads (concerns memory consumption,
choose smaller windows for higher coverage). In range [1..100000].
.IP
SNP calling options: :
.IP
Threshold method related: :
.HP
\fB\-mm\fR, \fB\-\-min\-mutations\fR NUM
.IP
Minimal number of observed mutations for mutation to be called.
.HP
\fB\-pt\fR, \fB\-\-perc\-threshold\fR NUM
.IP
Minimal percentage of mutational base for mutation to be called.
.HP
\fB\-mq\fR, \fB\-\-min\-quality\fR NUM
.IP
Minimal average quality of mutational base for mutation to be
called.
.IP
Maq method related: :
.HP
\fB\-th\fR, \fB\-\-theta\fR NUM
.IP
Dependency coefficient.
.HP
\fB\-hr\fR, \fB\-\-hetero\-rate\fR NUM
.IP
Heterozygote rate.
.HP
\fB\-mmq\fR, \fB\-\-min\-map\-quality\fR NUM
.IP
Minimum base call (mapping) quality for a match to be considered.
.HP
\fB\-ch\fR, \fB\-\-corrected\-het\fR
.IP
Use amplification bias corrected distribution for heterozygotes.
Default: off.
.HP
\fB\-maf\fR, \fB\-\-mean\-alleleFreq\fR NUM
.IP
Mean ref allele frequency in heterozygotes.
.HP
\fB\-ac\fR, \fB\-\-amp\-cycles\fR NUM
.IP
Number of amplification cycles.
.HP
\fB\-ae\fR, \fB\-\-amp\-efficiency\fR NUM
.IP
Polymerase efficiency, probability of amplification.
.HP
\fB\-in\fR, \fB\-\-initial\-N\fR NUM
.IP
Initial allele population size.
.HP
\fB\-mec\fR, \fB\-\-min\-explained\-column\fR NUM
.IP
Minimum fraction of alignment column reads explained by genotype
call.
.IP
Indel calling options: :
.HP
\fB\-it\fR, \fB\-\-indel\-threshold\fR NUM
.IP
Minimal number of indel\-supporting reads required for indel calling.
.HP
\fB\-ipt\fR, \fB\-\-indel\-perc\-threshold\fR NUM
.IP
Minimal ratio of indel\-supporting/covering reads for indel to be
called.
.HP
\fB\-iqt\fR, \fB\-\-indel\-quality\-thresh\fR NUM
.IP
Minimal average quality of inserted base/deletion\-neighboring bases
for indel to be called.
.HP
\fB\-bsi\fR, \fB\-\-both\-strands\-indel\fR
.IP
Both strands need to be observed for indel to be called. Default:
off.
.HP
\fB\-ebi\fR, \fB\-\-exclude\-border\-indel\fR NUM
.IP
Same as option \fB\-eb\fR but for indel candidates.
.IP
Other options: :
.HP
\fB\-lf\fR, \fB\-\-log\-file\fR FILE
.IP
Write log file to FILE.
.HP
\fB\-v\fR, \fB\-\-verbose\fR
.IP
Enable verbose output.
.HP
\fB\-vv\fR, \fB\-\-very\-verbose\fR
.IP
Enable very verbose output.
.HP
\fB\-q\fR, \fB\-\-quiet\fR
.IP
Set verbosity to a minimum.
.PP
VERSION
.IP
snp_store version: 1.0.1
Last update March 14, 2013