NAME

       snp_store - SnpStore

       SYNOPSIS

              snp_store [OPTIONS] "GENOME FILE" "MAPPED READ FILE(S)"

       DESCRIPTION

              SNP and Indel Calling in Mapped Read Data.

       -h, --help

              Displays this help message.

       --version

              Display version information

              Options: :

       -o, --output FILE

              Output file for SNPs (must be set, no default construction).

       -if, --input-format NUM

              Set  input  format:  0  for  GFF  format  and 1 for SAM format (both must be sorted
              according to genome positions). Default: 0.

       -of, --output-format NUM

              Set output format: 0 to output all  candidate  snps  amd  1  to  output  successful
              candidate snps only. Default: 0.

       -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 Ascii value - 64 (instead of Ascii - 33).

       -id, --indel-file FILE

              Output file for called indels in gff format. Default: off.

       -m, --method NUM

              Set  method  used  for  SNP  calling:  0 for threshold method and 1 for maq method.
              Default: 1.

       -mp, --max-pile NUM

              Maximal number of matches allowed to pile up at the same genome position.

       -mmp, --merged-max-pile

              Do pile up correction on merged lanes. Default: off.

       -mc, --min-coverage NUM

              Minimal required number of reads covering a candidate position.

       -fc, --force-call NUM

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

       -oa, --orientation-aware

              Distinguish between forward and reverse reads. Default: off.

       -mpr, --max-polymer-run NUM

              Discard indels in homopolymer runs longer than mpr.

       -dp, --diff-pos NUM

              Minimal number of different read positions supporting the mutation.

       -eb, --exclude-border NUM

              Exclude read positions within eb base pairs of read borders for SNV calling.

       -su, --suboptimal

              Keep suboptimal reads.

       -re, --realign

              Realign reads around indel candidates.

       -pws, --parse-window-size NUM

              Genomic  window size for parsing reads (concerns memory consumption, choose smaller
              windows for higher coverage). In range [1..100000].

              SNP calling options: :

              Threshold method related: :

       -mm, --min-mutations NUM

              Minimal number of observed mutations for mutation to be called.

       -pt, --perc-threshold NUM

              Minimal percentage of mutational base for mutation to be called.

       -mq, --min-quality NUM

              Minimal average quality of mutational base for mutation to be called.

              Maq method related: :

       -th, --theta NUM

              Dependency coefficient.

       -hr, --hetero-rate NUM

              Heterozygote rate.

       -mmq, --min-map-quality NUM

              Minimum base call (mapping) quality for a match to be considered.

       -ch, --corrected-het

              Use amplification bias corrected distribution for heterozygotes.  Default: off.

       -maf, --mean-alleleFreq NUM

              Mean ref allele frequency in heterozygotes.

       -ac, --amp-cycles NUM

              Number of amplification cycles.

       -ae, --amp-efficiency NUM

              Polymerase efficiency, probability of amplification.

       -in, --initial-N NUM

              Initial allele population size.

       -mec, --min-explained-column NUM

              Minimum fraction of alignment column reads explained by genotype call.

              Indel calling options: :

       -it, --indel-threshold NUM

              Minimal number of indel-supporting reads required for indel calling.

       -ipt, --indel-perc-threshold NUM

              Minimal ratio of indel-supporting/covering reads for indel to be called.

       -iqt, --indel-quality-thresh NUM

              Minimal average quality of inserted base/deletion-neighboring bases for indel to be
              called.

       -bsi, --both-strands-indel

              Both strands need to be observed for indel to be called. Default: off.

       -ebi, --exclude-border-indel NUM

              Same as option -eb but for indel candidates.

              Other options: :

       -lf, --log-file FILE

              Write log file to FILE.

       -v, --verbose

              Enable verbose output.

       -vv, --very-verbose

              Enable very verbose output.

       -q, --quiet

              Set verbosity to a minimum.

       VERSION

              snp_store version: 1.0.1 Last update March 14, 2013