## Utilities / Call SNPs and short INDELs

### Description

Calls SNPs and short INDELs for one or more diploid individuals.

### Parameters

- Reference sequence (human hg19, mouse mm9, rat rn4) [human hg19]
- Chromosome names in my BAM file look like (1, chr1) [chr1]
- Call variants only for a certain region (String) []
- Disable probabilistic realignment for computation of BAC (yes, no) [no]
- Downgrading coefficient (Integer) [0]
- Minimum mapping quality for an alignment to be used (Integer) [0]
- Minimum base quality for a base to be considered (Integer) [13]
- Output per sample read depth (yes, no) [no]
- Output per sample strand bias P-value (yes, no) [no]
- Call only SNPs, indels not considered (yes, no) [no]
- Skip sites where reference is ambiguous (yes, no) [no]
- Use maximum likelihood to score variants, and perform HWE analysis (yes, no) [no]
- Maximum read depth (Integer) [100]

### Details

You can provide your own reference sequence in FASTA format or choose one of the provided reference genomes. If you use the reference genomes provided by Chipster, please indicate the style of chromosome naming in your BAM file (e.g. chr1 or 1).

Alignment records are grouped by sample identifiers in @RG header lines. If sample identifiers are absent, each input file is regarded as one sample.

You can provide a coefficient for downgrading mapping quality for reads containing excessive mismatches. Given a read with a phred-scaled probability q of being generated from the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality. Applying this option usually helps BWA-short but may not other mappers. The recommended value for BWA is 50.

Maximum read depth should be adjusted to about twice the average read depth.

### Output

Output is a VCF file. You can view VCF files in Chipster as text (which includes the header) or spreadsheet (which can be shorted). The location column in the spreadsheet can be used in Chipster genome browser to navigate quickly through a list of variants.

### References

This tool is based on the SAMtools package. Please cite the article The Sequence alignment/map (SAM) format and SAMtools by Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) Bioinformatics, 25, 2078-9. [PMID: 19505943].