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cat trios_tutorial.all.samtools.vcf | headtail -10000 | awk '{if ($6>500) {print $2"\t"$10"\t"$11"\t"$12}}' | grep "0/0" | sed s/':'/' \t'/g | awk '{print $2"\t"$5$4"\t"$8$6}' | tail -100 | sort | uniq -c | sort -n -r |
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Here are the steps going into this command:
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12 0/0 0/1 0/0 5 0/0 0/1 0/1 3 0/1 0/0 0/0 4 0/1 0/0 0/1 8 0/1 0/0 1/1 43 0/1 0/1 0/0 24 0/1 1/1 0/0 1 1/1 0/1 0 34 0/1 0/1 0/0 20 0/1 0/0 0/1 20 0/0 0/1 0/0 14 0/1 1/1 0/0 6 0/0 0/1 0/1 4 1/1 1/1 0/0 1 1/1 0/1 0/0 1 0/1 0/0 0/0 |
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Here is my interpretation of the data: 1) This method effectively looks at a very narrow genomic region, probably within a homologous recombination block. 2) The most telling data: the child will have heterozygous SNPs from two homozygous parents. 3) So all this data is consistent with column 1 (NA12878) being the child: 12 0/0 0/1 0/0 "Outlier" data are: 3 0/1 0/0 0/0 1 1/1 0/1 0/0 This is, in fact, the correct assessment - NA12878 is the child. |
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