Call variants in UGENE can be done using SAMtools mpileup and bcftools view utilities. To read additional information about SAMtools and its utilities visit SAMTools SAMtools homepage. Both utilities are embedded into UGENE and there is no need in additional configuration.
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The next page allows one to configure SAMtools vcfutils parameters:
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Log filtered | Print filtered variants into the log (varFilter) (-p). |
Minimum RMS quality | Minimum RMS mapping quality for SNPs (varFilter) (-Q). |
Minimum read depth | Minimum read depth (varFilter) (-d). |
Maximum read depth | Maximum read depth (varFilter) (-D). |
Alternate bases | Minimum number of alternate bases (varFilter) (-a). |
Gap size | SNP within INT bp around a gap to be filtered (varFilter) (-w). |
Window size | Window size for filtering adjacent gaps (varFilter) (-W). |
Strand bias | Minimum P-value for strand bias (given PV4) (varFilter) (-1). |
BaseQ bias | Minimum P-value for baseQ bias (varFilter) (-2). |
MapQ bias | Minimum P-value for mapQ bias (varFilter) (-3). |
End distance bias | Minimum P-value for end distance bias (varFilter) (-4). |
HWE | Minimum P-value for HWE (plus F<0) (varFilter) (-e). |
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<center> <br> <img src="/wiki/download/attachments/3244617/Call variants with SAMtools_6.png"/> <br> </center> |
On this page you should select an output file. Set required parameters and click the Finish button.
Note that default button reverts all parameters to default settings.
Now let’s validate and run the workflow. To validate that the workflow is correct and all parameters are set properly click the Validate workflow button on the Workflow Designer toolbar:
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<center> <br> <img src="/wiki/download/attachments/3244617/Call variants with SAMtools_7.png"/> <br> </center> |
If there are some errors, they will be shown in the Error list at the bottom of the Workflow Designer window, for example:
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The dashboard will contain information about workflow: input and output files, all information about task. .
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The work on this pipeline was supported by grant RUB1-31097-NO-12 from NIAID. |