snp_store - SnpStore

       SNP and Indel Calling in Mapped Read Data.

snp_store-mc2-it2exampleGenome.faexampleReads.gff-oexampleSNPs.vcf-idexampleIndels.gff
              Call  SNPs and indels of a low-coverage example (minimum coverage and indel threshold were reduced
              to 2).

       snp_store-re-mc2-it2exampleGenome.faexampleReads.gff-oexampleSNPs.vcf-idexampleIndels.gff
              Computes a realignment before variant calling. Now, the two 1bp insertions should have been merged
              into one 2bp insertion.

snp_store 1.3.8 [tarball]                                                                           SNP_STORE(1)

       snp_store - SnpStore

-h, --help
              Display the help message.

       --version
              Display version information.

   MainOptions:-o, --outputOUTPUT_FILE
              SNP output file (mandatory). Valid filetype is: .vcf.

       -osc, --only-successful-candidates
              Output only successfully called SNP candidates. Default: Output all candidates.

       -dc, --dont-clip
              Ignore clip tags in gff. Default: off.

       -mu, --multi
              Keep non-unique fragmentStore.alignedReadStore. Default: off.

       -hq, --hide-qualities
              Only show coverage (no qualities) in SNP output file. Default: off.

       -sqo, --solexa-qual-offset
              Base qualities are encoded as char value - 64 (instead of char - 33).

       -id, --indel-fileOUTPUT_FILE
              Output file for called indels in gff format. Default: off. Valid filetype is: .gff.

       -m, --methodSTRING
              Set method used for SNP calling either threshold based or Maq  method.  One  of  thresh  and  maq.
              Default: maq.

       -mp, --max-pileINTEGER
              Maximal  number  of  matches  allowed  to  pile up at the same genome position. In range [1..inf].
              Default: 1.

       -mmp, --merged-max-pile
              Do pile up correction on merged lanes. Default: off.

       -mc, --min-coverageINTEGER
              Minimal required number of reads covering a candidate position. In range [1..inf]. Default: 5.

       -fc, --force-callINTEGER
              Always call base if count is >= fc, ignore other parameters.  Default:  off.  In  range  [1..inf].
              Default: 10.

       -oa, --orientation-aware
              Distinguish between forward and reverse reads. Default: off.

       -mpr, --max-polymer-runINTEGER
              Discard indels in homopolymer runs longer than mpr. In range [0..inf]. Default: 100.

       -dp, --diff-posINTEGER
              Minimal number of different read positions supporting the mutation. In range [0..inf]. Default: 0.

       -eb, --exclude-borderINTEGER
              Exclude  read  positions  within  eb  base pairs of read borders for SNV calling. Default: off. In
              range [0..inf]. Default: 0.

       -su, --suboptimal
              Keep suboptimal reads. Default: off

       -re, --realign
              Realign reads around indel candidates. Default: off

       -pws, --parse-window-sizeINTEGER
              Genomic window size for parsing reads (concerns memory consumption,  choose  smaller  windows  for
              higher coverage). In range [1..inf]. Default: 1000000.

   Thresholdmethodrelated:-mm, --min-mutationsINTEGER
              Minimal number of observed mutations for mutation to be called. In range [1..inf]. Default: 3.

       -pt, --perc-thresholdDOUBLE
              Minimal percentage of mutational base for mutation to be called. In range [0..inf]. Default: 0.25.

       -mq, --min-qualityDOUBLE
              Minimal  average quality of mutational base for mutation to be called. In range [0..inf]. Default:
              10.

   Maqmethodrelated:-th, --thetaDOUBLE
              Dependency coefficient. In range [0..inf]. Default: 0.85.

       -hr, --hetero-rateDOUBLE
              Heterozygote rate. In range [0..1]. Default: 0.001.

       -mmq, --min-map-qualityINTEGER
              Minimum base call (mapping) quality for a match to be considered. In range [0..inf]. Default: 1.

       -ch, --corrected-het
              Use amplification bias corrected distribution for heterozygotes. Default: off.

       -maf, --mean-alleleFreqDOUBLE
              Mean ref allele frequency in heterozygotes. In range [0..inf]. Default: 0.51.

       -ac, --amp-cyclesINTEGER
              Number of amplification cycles. In range [0..inf]. Default: 18.

       -ae, --amp-efficiencyDOUBLE
              Polymerase efficiency, probability of amplification. In range [0..1]. Default: 0.3.

       -in, --initial-NINTEGER
              Initial allele population size. In range [0..inf]. Default: 10.

       -mec, --min-explained-columnDOUBLE
              Minimum fraction of alignment column reads explained by genotype call. In range  [0..1].  Default:
              0.8.

   Indelcallingoptions:-it, --indel-thresholdINTEGER
              Minimal  number  of indel-supporting reads required for indel calling. In range [1..inf]. Default:
              3.

       -ipt, --indel-perc-thresholdDOUBLE
              Minimal ratio of indel-supporting/covering reads for indel to be called. In range [0..1]. Default:
              0.25.

       -iqt, --indel-quality-threshINTEGER
              Minimal average quality of inserted base/deletion-neighboring bases for indel  to  be  called.  In
              range [0..inf]. Default: 1.

       -bsi, --both-strands-indel
              Both strands need to be observed for indel to be called. Default: off.

       -ebi, --exclude-border-indelINTEGER
              Same as option -eb but for indel candidates. In range [0..inf]. Default: 0.

   Otheroptions:-lf, --log-fileSTRING
              Write log to FILE.

       -v, --verbose
              Enable verbose output.

       -vv, --very-verbose
              Enable very verbose output.

       -q, --quiet
              Set verbosity to a minimum.

GENOMEINPUT_FILE
              A reference genome file. Valid filetypes are: .fasta and .fa.

       ALIGNMENTS List of INPUT_FILE's
              Read  alignment file(s) sorted by genomic position. Valid filetypes are: .sam[.*], .gff, and .bam,
              where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.

snp_store [OPTIONS] <GENOMEFILE> <ALIGNMENTFILE> [<ALIGNMENTFILE> ...]