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SNPest specifications
Information
| Unique identifier | OMICS_08845 |
|---|---|
| Name | SNPest |
| Software type | Package/Module |
| Interface | Command line interface |
| Restrictions to use | None |
| Input data | SNPest takes input generated by the “samtools mpileup -s” command (or equivalent) reporting nucleotides mapped to each position together with read qualities and mapping qualities. |
| Output data | The output is in VCF format with a line per position covered in the genome. |
| Operating system | Unix/Linux, Mac OS |
| Programming languages | C++, Perl |
| License | GNU General Public License version 2.0 |
| Computer skills | Advanced |
| Stability | Stable |
| Maintained | Yes |
Versioning
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Documentation
Maintainer
- person_outline Stinus Lindgreen <>
Publications for SNPest
SNPest in pipeline
[…] with default parameters (). the bam files were processed using samtools (-q 25 -q 0) to generate mpileup output (). this output was used to create high-confidence genotypes for each strain using snpest v. 1.0 (minimum depth of 10 reads, minimum posterior probability of 0.999, minimum support for indel of 90%) (). the reference embl file was processed using an in-house script to extract […]
SNPest in publications
(2)[…] with default parameters (). the bam files were processed using samtools (-q 25 -q 0) to generate mpileup output (). this output was used to create high-confidence genotypes for each strain using snpest v. 1.0 (minimum depth of 10 reads, minimum posterior probability of 0.999, minimum support for indel of 90%) (). the reference embl file was processed using an in-house script to extract […]
[…] or only for mtdna. such algorithms report the probabilities of different types of postmortem dna degradation, which allows for better statistical modelling at the variant calling stage, employing snpest or custom scripts. a typical ngs pipeline for adna analysis is shown in . figure 3. , the amount of extracted endogenous dna may allow satisfactory coverage of adna sequences (as high […]
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