This is the command snp_store that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
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