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, 15:27, 20 February 2014
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| =Analyses= | | =Analyses= |
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| + | ==File Preparation== |
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| + | The VCF file you work with should preferably be BCF2.1 compatible. Here we provide an example in /net/fantasia/home/atks/indel_analysis_tutorial. \\ |
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| + | To convert to BCF format which will work fast with vt: |
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| + | vt view mills.vcf -o mills.bcf |
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| + | You will encounter an error as the header does not contain contigs. To fix this, you should construct a complete header for mills.vcf. This is done for you in mills.with.alt.hdr.* |
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| + | vt view mills.with.alt.hdr.vcf -o mills.genotypes.bcf |
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| + | To index: |
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| + | vt index mills.genotypes.bcf |
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| + | To extract just the site list which is convenient for working with if you are not analysing the genotypes of the individuals |
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| + | vt view -s mills.genotypes.bcf -o mills.sites.bcf |
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| + | To index: |
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| + | vt index mills.sites.bcf |
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| + | You may also work with vcf.gz, just name the output as *.vcf.gz. But it will be slower with vt. |
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| ==Normalization== | | ==Normalization== |