NAME

       snp_store - SnpStore

SYNOPSIS

       snp_store [OPTIONS] <GENOME FILE> <ALIGNMENT FILE> [<ALIGNMENT FILE> ...]

DESCRIPTION

       SNP and Indel Calling in Mapped Read Data.

REQUIRED ARGUMENTS

       GENOME INPUT_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.

OPTIONS

       -h, --help
              Display the help message.

       --version
              Display version information.

   Main Options:
       -o, --output OUTPUT_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-file OUTPUT_FILE
              Output file for called indels in gff format. Default: off. Valid filetype is: .gff.

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

       -mp, --max-pile INTEGER
              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-coverage INTEGER
              Minimal  required number of reads covering a candidate position. In range [1..inf].
              Default: 5.

       -fc, --force-call INTEGER
              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-run INTEGER
              Discard  indels  in  homopolymer  runs longer than mpr. In range [0..inf]. Default:
              100.

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

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

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

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

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

   Maq method related:
       -th, --theta DOUBLE
              Dependency coefficient. In range [0..inf]. Default: 0.85.

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

       -mmq, --min-map-quality INTEGER
              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-alleleFreq DOUBLE
              Mean ref allele frequency in heterozygotes. In range [0..inf]. Default: 0.51.

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

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

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

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

   Indel calling options:
       -it, --indel-threshold INTEGER
              Minimal number of indel-supporting reads  required  for  indel  calling.  In  range
              [1..inf]. Default: 3.

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

       -iqt, --indel-quality-thresh INTEGER
              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-indel INTEGER
              Same as option -eb but for indel candidates. In range [0..inf]. Default: 0.

   Other options:
       -lf, --log-file STRING
              Write log to FILE.

       -v, --verbose
              Enable verbose output.

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

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

EXAMPLES

       snp_store   -mc   2   -it  2  exampleGenome.fa  exampleReads.gff  -o  exampleSNPs.vcf  -id
       exampleIndels.gff
              Call SNPs and  indels  of  a  low-coverage  example  (minimum  coverage  and  indel
              threshold were reduced to 2).

       snp_store  -re  -mc  2  -it  2  exampleGenome.fa  exampleReads.gff  -o exampleSNPs.vcf -id
       exampleIndels.gff
              Computes a realignment before variant calling. Now, the two 1bp  insertions  should
              have been merged into one 2bp insertion.