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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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1234 0/01 0/1 0/0 520 0/01 0/10 0/1 20 3 0/10 0/01 0/0 14 4 0/1 01/01 0/10 86 0/10 0/1 0 1/1 43 4 01/1 01/1 0/0 241 01/1 10/1 0/0 1 10/1 0/10 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 Overall this data is consistent with column 1 (NA12878) being the child. Lines marked with an * are inconsistant: 12 34 0/01 0/1 0/0 "Outlier" data are: * No mendelian combination exists 31 01/1 0/01 0/0 * 1 10/1 0/10 0/0 * This is, in fact, the correct assessment - NA12878 is the child. |
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