Man page - snp_store(1)
Packages contains this manual
- rabema_evaluate(1)
- alf(1)
- mason_materializer(1)
- pair_align(1)
- gustaf(1)
- stellar(1)
- razers3(1)
- sak(1)
- yara_indexer(1)
- mason_frag_sequencing(1)
- micro_razers(1)
- rabema_prepare_sam(1)
- insegt(1)
- rabema_build_gold_standard(1)
- splazers(1)
- seqan_tcoffee(1)
- yara_mapper(1)
- tree_recon(1)
- mason_genome(1)
- mason_methylation(1)
- razers(1)
- snp_store(1)
apt-get install seqan-apps
Manual
SNP_STORE
NAMESYNOPSIS
DESCRIPTION
REQUIRED ARGUMENTS
OPTIONS
Main Options:
Threshold method related:
Maq method related:
Indel calling options:
Other options:
EXAMPLES
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.