.TH SNP_STORE 1 "" "snp_store 1.3.8 [tarball]" ""
.SH NAME
snp_store \- SnpStore
.SH SYNOPSIS
\fBsnp_store\fP [\fIOPTIONS\fP] <\fIGENOME FILE\fP> <\fIALIGNMENT FILE\fP> [<\fIALIGNMENT FILE\fP> ...]
.SH DESCRIPTION
SNP and Indel Calling in Mapped Read Data.
.SH REQUIRED ARGUMENTS
.TP
\fBGENOME\fP \fIINPUT_FILE\fP
A reference genome file. Valid filetypes are: \fI.fasta\fP and \fI.fa\fP.
.TP
\fBALIGNMENTS\fP List of \fIINPUT_FILE\fP's
Read alignment file(s) sorted by genomic position. Valid filetypes are: \fI.sam[.*]\fP, \fI.gff\fP, and \fI.bam\fP, where * is any of the following extensions: \fIgz\fP, \fIbz2\fP, and \fIbgzf\fP for transparent (de)compression.
.SH OPTIONS
.TP
\fB-h\fP, \fB--help\fP
Display the help message.
.TP
\fB--version\fP
Display version information.
.SS Main Options:
.TP
\fB-o\fP, \fB--output\fP \fIOUTPUT_FILE\fP
SNP output file (mandatory). Valid filetype is: \fI.vcf\fP.
.TP
\fB-osc\fP, \fB--only-successful-candidates\fP
Output only successfully called SNP candidates. Default: Output all candidates.
.TP
\fB-dc\fP, \fB--dont-clip\fP
Ignore clip tags in gff. Default: off.
.TP
\fB-mu\fP, \fB--multi\fP
Keep non-unique fragmentStore.alignedReadStore. Default: off.
.TP
\fB-hq\fP, \fB--hide-qualities\fP
Only show coverage (no qualities) in SNP output file. Default: off.
.TP
\fB-sqo\fP, \fB--solexa-qual-offset\fP
Base qualities are encoded as char value - 64 (instead of char - 33).
.TP
\fB-id\fP, \fB--indel-file\fP \fIOUTPUT_FILE\fP
Output file for called indels in gff format. Default: off. Valid filetype is: \fI.gff\fP.
.TP
\fB-m\fP, \fB--method\fP \fISTRING\fP
Set method used for SNP calling either threshold based or Maq method. One of \fIthresh\fP and \fImaq\fP. Default: \fImaq\fP.
.TP
\fB-mp\fP, \fB--max-pile\fP \fIINTEGER\fP
Maximal number of matches allowed to pile up at the same genome position. In range [1..inf]. Default: \fI1\fP.
.TP
\fB-mmp\fP, \fB--merged-max-pile\fP
Do pile up correction on merged lanes. Default: off.
.TP
\fB-mc\fP, \fB--min-coverage\fP \fIINTEGER\fP
Minimal required number of reads covering a candidate position. In range [1..inf]. Default: \fI5\fP.
.TP
\fB-fc\fP, \fB--force-call\fP \fIINTEGER\fP
Always call base if count is >= fc, ignore other parameters. Default: off. In range [1..inf]. Default: \fI10\fP.
.TP
\fB-oa\fP, \fB--orientation-aware\fP
Distinguish between forward and reverse reads. Default: off.
.TP
\fB-mpr\fP, \fB--max-polymer-run\fP \fIINTEGER\fP
Discard indels in homopolymer runs longer than mpr. In range [0..inf]. Default: \fI100\fP.
.TP
\fB-dp\fP, \fB--diff-pos\fP \fIINTEGER\fP
Minimal number of different read positions supporting the mutation. In range [0..inf]. Default: \fI0\fP.
.TP
\fB-eb\fP, \fB--exclude-border\fP \fIINTEGER\fP
Exclude read positions within eb base pairs of read borders for SNV calling. Default: off. In range [0..inf]. Default: \fI0\fP.
.TP
\fB-su\fP, \fB--suboptimal\fP
Keep suboptimal reads. Default: off
.TP
\fB-re\fP, \fB--realign\fP
Realign reads around indel candidates. Default: off
.TP
\fB-pws\fP, \fB--parse-window-size\fP \fIINTEGER\fP
Genomic window size for parsing reads (concerns memory consumption, choose smaller windows for higher coverage). In range [1..inf]. Default: \fI1000000\fP.
.SS  Threshold method related:
.TP
\fB-mm\fP, \fB--min-mutations\fP \fIINTEGER\fP
Minimal number of observed mutations for mutation to be called. In range [1..inf]. Default: \fI3\fP.
.TP
\fB-pt\fP, \fB--perc-threshold\fP \fIDOUBLE\fP
Minimal percentage of mutational base for mutation to be called. In range [0..inf]. Default: \fI0.25\fP.
.TP
\fB-mq\fP, \fB--min-quality\fP \fIDOUBLE\fP
Minimal average quality of mutational base for mutation to be called. In range [0..inf]. Default: \fI10\fP.
.SS  Maq method related:
.TP
\fB-th\fP, \fB--theta\fP \fIDOUBLE\fP
Dependency coefficient. In range [0..inf]. Default: \fI0.85\fP.
.TP
\fB-hr\fP, \fB--hetero-rate\fP \fIDOUBLE\fP
Heterozygote rate. In range [0..1]. Default: \fI0.001\fP.
.TP
\fB-mmq\fP, \fB--min-map-quality\fP \fIINTEGER\fP
Minimum base call (mapping) quality for a match to be considered. In range [0..inf]. Default: \fI1\fP.
.TP
\fB-ch\fP, \fB--corrected-het\fP
Use amplification bias corrected distribution for heterozygotes. Default: off.
.TP
\fB-maf\fP, \fB--mean-alleleFreq\fP \fIDOUBLE\fP
Mean ref allele frequency in heterozygotes. In range [0..inf]. Default: \fI0.51\fP.
.TP
\fB-ac\fP, \fB--amp-cycles\fP \fIINTEGER\fP
Number of amplification cycles. In range [0..inf]. Default: \fI18\fP.
.TP
\fB-ae\fP, \fB--amp-efficiency\fP \fIDOUBLE\fP
Polymerase efficiency, probability of amplification. In range [0..1]. Default: \fI0.3\fP.
.TP
\fB-in\fP, \fB--initial-N\fP \fIINTEGER\fP
Initial allele population size. In range [0..inf]. Default: \fI10\fP.
.TP
\fB-mec\fP, \fB--min-explained-column\fP \fIDOUBLE\fP
Minimum fraction of alignment column reads explained by genotype call. In range [0..1]. Default: \fI0.8\fP.
.SS Indel calling options:
.TP
\fB-it\fP, \fB--indel-threshold\fP \fIINTEGER\fP
Minimal number of indel-supporting reads required for indel calling. In range [1..inf]. Default: \fI3\fP.
.TP
\fB-ipt\fP, \fB--indel-perc-threshold\fP \fIDOUBLE\fP
Minimal ratio of indel-supporting/covering reads for indel to be called. In range [0..1]. Default: \fI0.25\fP.
.TP
\fB-iqt\fP, \fB--indel-quality-thresh\fP \fIINTEGER\fP
Minimal average quality of inserted base/deletion-neighboring bases for indel to be called. In range [0..inf]. Default: \fI1\fP.
.TP
\fB-bsi\fP, \fB--both-strands-indel\fP
Both strands need to be observed for indel to be called. Default: off.
.TP
\fB-ebi\fP, \fB--exclude-border-indel\fP \fIINTEGER\fP
Same as option -eb but for indel candidates. In range [0..inf]. Default: \fI0\fP.
.SS Other options:
.TP
\fB-lf\fP, \fB--log-file\fP \fISTRING\fP
Write log to FILE.
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\fB-v\fP, \fB--verbose\fP
Enable verbose output.
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\fB-vv\fP, \fB--very-verbose\fP
Enable very verbose output.
.TP
\fB-q\fP, \fB--quiet\fP
Set verbosity to a minimum.
.SH EXAMPLES
.TP
\fBsnp_store\fP \fB-mc\fP \fB2\fP \fB-it\fP \fB2\fP \fBexampleGenome.fa\fP \fBexampleReads.gff\fP \fB-o\fP \fBexampleSNPs.vcf\fP \fB-id\fP \fBexampleIndels.gff\fP
Call SNPs and indels of a low-coverage example (minimum coverage and indel threshold were reduced to 2).
.TP
\fBsnp_store\fP \fB-re\fP \fB-mc\fP \fB2\fP \fB-it\fP \fB2\fP \fBexampleGenome.fa\fP \fBexampleReads.gff\fP \fB-o\fP \fBexampleSNPs.vcf\fP \fB-id\fP \fBexampleIndels.gff\fP
Computes a realignment before variant calling. Now, the two 1bp insertions should have been merged into one 2bp insertion.