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.
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.