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snp_store - SnpStore




SNP and Indel Calling in Mapped Read Data.


A reference genome file. Valid filetypes are: .fasta and .fa.
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.


-h, --help
Display the help message.
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.


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.
snp_store 1.3.8 [tarball]