table of contents
- stretch 2.3.1+dfsg-4
- testing 2.4.0+dfsg-11
- stretch-backports 2.4.0+dfsg-11~bpo9+1
- unstable 2.4.0+dfsg-11
SNP_STORE(1) | User Commands | SNP_STORE(1) |
NAMEΒΆ
snp_store - SnpStoreSYNOPSIS
- 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 and bgzf for transparent (de)compression.
OPTIONS
-h, --help
- Display the help message.
--version-check BOOL
- Turn this option off to disable version update notifications of the application. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: 1.
--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.
VERSION
- Last update: snp_store version: 1.3.6 [tarball] SeqAn version: 2.3.1
June 2017 | snp_store 2.3.1+dfsg-4 |