Exome-seq / Call SNPs and short INDELs for one diploid individual

Description

Call SNPs and short INDELs for one diploid individual.

Parameters

Details

You can provide your own reference sequence in FASTA format or choose one of the provided reference genomes. 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.

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].