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, 20:33, 15 June 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. \\
| + | vt peek all.genotypes.bcf |
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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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| − | === A quick summary ===
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| − | atks@1000g:~/dev/vt/comparisons/seq_workshop$ vt peek run/final/all.genotypes.bcf
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| − | peek v0.5
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| | options: input VCF file run/final/all.genotypes.bcf | | options: input VCF file run/final/all.genotypes.bcf |
