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SNP_STORE(1) User Commands SNP_STORE(1)

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
September 2014 snp_store 1.4.1+dfsg