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17 bytes added
, 15:42, 9 July 2014
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| The following section details some simple analyses we can perform. | | The following section details some simple analyses we can perform. |
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− | | + | ===Summary=== |
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| First you want to know what is in the vcf file. | | First you want to know what is in the vcf file. |
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| ${GC}/bin/vt peek ${OUT}/final/all.genotypes.vcf.gz -f "FILTER.PASS&&(LEN==4||DLEN==3)" | | ${GC}/bin/vt peek ${OUT}/final/all.genotypes.vcf.gz -f "FILTER.PASS&&(LEN==4||DLEN==3)" |
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− | == Comparison with other data sets == | + | === Comparison with other data sets === |
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| It is usually useful to examine the call sets against known data sets for the passed variants. | | It is usually useful to examine the call sets against known data sets for the passed variants. |
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| This analysis supports filters too. | | This analysis supports filters too. |
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− | ==Normalization== | + | ===Normalization=== |
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| A slight digression here, when analyzing indels, it is important to normalize it. While it is a simple concept, | | A slight digression here, when analyzing indels, it is important to normalize it. While it is a simple concept, |