snpPosOnSource (1)

Adds pos_source to snp

Carta.tech
Man Pages
Executable programs or shell commands
snpPosOnSource: Adds pos_source to snp

Carta.tech
Packages
mipe
snpPosOnSource: Adds pos_source to snp

SYNOPSIS

snpPosOnSource.pl your_file.mipe < my_data.txt

ADDITIONAL INFO

See http://mipe.sourceforge.net

AUTHOR

Jan Aerts ([email protected])

snpPosOnDesign.1: Adds pos_design to snp
snp_store.1: 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