---
name: "snp_store"
section: "1"
platform: "linux"
package: "seqan-apps"
version: "2.4.0+dfsg-16"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/snp_store"
---

# snp\_store(1)

SnpStore

## 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.