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, 10:22, 26 October 2016
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| | ** Note: In the VCF file either PL or GL has to be provided, and only the PL (or GL) field is used in the calling. | | ** Note: In the VCF file either PL or GL has to be provided, and only the PL (or GL) field is used in the calling. |
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| − | * A map file in the PLINK format. See blow for examples how to generate a high quality map file. | + | * A map file in the PLINK format. See blow for examples how to generate a map file with common and high quality variants |
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| | == Examples of generating the map file == | | == Examples of generating the map file == |
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| | == Filtering == | | == Filtering == |
| − | We recommend two filtering strategies. The first is a simple filtering and the second one is more advance. Please see the triodenovo page below for more information: | + | We recommend two filtering strategies. The first is a simple filtering and the second one is more advanced. Please see the triodenovo page below for more information: |
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| | http://genome.sph.umich.edu/wiki/Triodenovo | | http://genome.sph.umich.edu/wiki/Triodenovo |
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| − | 3. Further thoughts about filtering for SNVs without bam files (step 2 requires bam files). There is no consensus on filtering so this can be very flexible.
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| − | * If you have a multi-sample call VCF it may be helpful to select those mutation candidates that appear only once in your VCF (AC=1 for example). This can be the top tier to consider. Relaxing AC to 2 or 3 can recover more real mutations but also increase false positives.
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| − | * If it is too stringent to filter out known sites, it may be helpful to select candidates that have low (e.g. <0.002)1000G or ESP allele frequencies. Some mutations can occur on know variant sites but mutations with high population frequencies may not be of great interest, if indeed they are real.
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| − | * Candidates in segmental duplications, low complexity regions or other copy number regions may be flagged for further analysis.
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| − | * Candidates for which parents are not hom-ref or offspring is a double mutant are more likely to be due to artifacts so the interpretation of these candidates may require additional QC if they appear to be interesting to the investigators.
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| | == Download == | | == Download == |
