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| SNP_STORE(1) |
|
SNP_STORE(1) |
NAME¶
snp_store - SnpStore
SYNOPSIS¶
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, bz2, and bgzf for
transparent (de)compression.
OPTIONS¶
- -h, --help
- Display the help message.
- --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.
- -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.
- -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.
