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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.


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Main Options:

SNP output file (mandatory). Valid filetype is: .vcf.
Output only successfully called SNP candidates. Default: Output all candidates.
Ignore clip tags in gff. Default: off.
Keep non-unique fragmentStore.alignedReadStore. Default: off.
Only show coverage (no qualities) in SNP output file. Default: off.
Base qualities are encoded as char value - 64 (instead of char - 33).
Output file for called indels in gff format. Default: off. Valid filetype is: .gff.
Set method used for SNP calling either threshold based or Maq method. One of thresh and maq. Default: maq.
Maximal number of matches allowed to pile up at the same genome position. In range [1..inf]. Default: 1.
Do pile up correction on merged lanes. Default: off.
Minimal required number of reads covering a candidate position. In range [1..inf]. Default: 5.
Always call base if count is >= fc, ignore other parameters. Default: off. In range [1..inf]. Default: 10.
Distinguish between forward and reverse reads. Default: off.
Discard indels in homopolymer runs longer than mpr. In range [0..inf]. Default: 100.
Minimal number of different read positions supporting the mutation. In range [0..inf]. Default: 0.
Exclude read positions within eb base pairs of read borders for SNV calling. Default: off. In range [0..inf]. Default: 0.
Keep suboptimal reads. Default: off
Realign reads around indel candidates. Default: off
Genomic window size for parsing reads (concerns memory consumption, choose smaller windows for higher coverage). In range [1..inf]. Default: 1000000.

Threshold method related:

Minimal number of observed mutations for mutation to be called. In range [1..inf]. Default: 3.
Minimal percentage of mutational base for mutation to be called. In range [0..inf]. Default: 0.25.
Minimal average quality of mutational base for mutation to be called. In range [0..inf]. Default: 10.

Maq method related:

Dependency coefficient. In range [0..inf]. Default: 0.85.
Heterozygote rate. In range [0..1]. Default: 0.001.
Minimum base call (mapping) quality for a match to be considered. In range [0..inf]. Default: 1.
Use amplification bias corrected distribution for heterozygotes. Default: off.
Mean ref allele frequency in heterozygotes. In range [0..inf]. Default: 0.51.
Number of amplification cycles. In range [0..inf]. Default: 18.
Polymerase efficiency, probability of amplification. In range [0..1]. Default: 0.3.
Initial allele population size. In range [0..inf]. Default: 10.
Minimum fraction of alignment column reads explained by genotype call. In range [0..1]. Default: 0.8.

Indel calling options:

Minimal number of indel-supporting reads required for indel calling. In range [1..inf]. Default: 3.
Minimal ratio of indel-supporting/covering reads for indel to be called. In range [0..1]. Default: 0.25.
Minimal average quality of inserted base/deletion-neighboring bases for indel to be called. In range [0..inf]. Default: 1.
Both strands need to be observed for indel to be called. Default: off.
Same as option -eb but for indel candidates. In range [0..inf]. Default: 0.

Other options:

Write log to FILE.
Enable verbose output.
Enable very verbose output.
Set verbosity to a minimum.


Call SNPs and indels of a low-coverage example (minimum coverage and indel threshold were reduced to 2).
Computes a realignment before variant calling. Now, the two 1bp insertions should have been merged into one 2bp insertion.
snp_store 1.3.7 [tarball]