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Retain all possible alternative | Retain all possible alternate alleles at variant sites. By default, the view command discards unlikely alleles. |
Indicate PL | Indicate PL is generated by r921 or before (ordering is different). |
No genotype information | Suppress all individual genotype information. |
A/C/G/T only | Skip sites where the REF field is not A/C/G/T. |
List of sites | List of sites at which information are outputted. |
QCALL likelihood | Output the QCALL likelihood format. |
List of samples | List of samples to use. The first column in the input gives the sample names and the second gives the ploidy, which can only be 1 or 2. When the 2nd column is absent, the sample ploidy is assumed to be 2. In the output, the ordering of samples will be identical to the one in FILE. |
Min samples fraction | Skip loci where the fraction of samples covered by reads is below FLOAT. |
Per-sample genotypes | Call per-sample genotypes at variant sites. |
INDEL-to-SNP Ratio | Ratio of INDEL-to-SNP mutation rate. |
Gap open error | Phred-scaled gap open sequencing error probability. Reducing INT leads to more indel calls. |
Max P(ref|D) | A site is considered to be a variant if P(ref|D). |
Pair/trio calling | Enable pair/trio calling. For trio calling, option -s is usually needed to be applied to configure the trio members and their ordering. In the file supplied to the option -s, the first sample must be the child, the second the father and the third the mother. The valid values of STR are “pair”, “trioauto”, “trioxd” and “trioxs”, where “pair” calls differences between two input samples, and “trioxd” (“trioxs”) specifies that the input is from the X chromosome non-PAR regions and the child is a female (male). |
N group-1 samples | Number of group-1 samples. This option is used for dividing the samples into two groups for contrast SNP calling or association test. When this option is in use, the following VCF INFO will be outputted: PC2, PCHI2 and QCHI2. |
N permutations | Number of permutations for association test (effective only with -1). |
Max P(chi^2) | Only perform permutations for P(chi^2). |
Choose these parameters and click the Next button. The last next page of the wizard appears:
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<center> <br> <img src="/wiki/download/attachments/3244617/Call variants with SAMtools_5.png"/> <br> </center> |
On this page you should select an output file. Optionally, you may also modify other parameters:
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Output file
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Location of the output data file.
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Document format
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Document format of output file.
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Existing file
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If a target file already exists, you can specify how it should be handled: overwrite, rename or append the output (if supported by the file format). If Rename option is choosen, existing file will be renamed.
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For example:
Click the browse button (“...”), select a directory and input file name “out_variations.snp”.
The next page allows one to configure SAMtools vcfutils parameters:
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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<img src="/wiki/download/attachments/3244617/Call variants with SAMtools_6.png"/>
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On this page you should select an output file. Set required parameters and click the Finish button.
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Now let’s validate and run the
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workflow. To validate that the
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workflow is correct and all parameters are set properly click the Validate
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workflow button on the Workflow Designer toolbar:
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<center>
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<img src="/wiki/download/attachments/3244617/Call variants with SAMtools_7.png"/>
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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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<center>
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<img src="/wiki/download/attachments/3244617/Call variants with SAMtools_8.png"/>
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However, if you have set all the required parameters, then there shouldn’t be errors.
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To run a valid
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workflow, click the Run
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workflow button on the Workflow Designer toolbar:
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<center>
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<img src="/wiki/download/attachments/3244617/Call variants with SAMtools_9.png"/>
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As soon as the variants calling task is finished, a notification will appear at the right bottom corner of the UGENE window. Click on the notification and select an appropriate task report:
The task report will contain a link to the output file with variations.
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