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Revision as of 10:39, 9 December 2014
, 10:39, 9 December 2014→Looking at final INDEL VCF
This gives use 588,566 indels with an insertion deletion ratio of 0.87.
This gives use 588,566 indels with an insertion deletion ratio of 0.87.
We next look at the filtered set. The PASS filter extracts all non overlapping variants and the INFO.AC!=0 extracts all indels that are either heterozygous or homozygous alternative.
We next look at the filtered set. The PASS filter reduces the setof indels to a non overlapping set and the INFO.AC!=0 extracts all indels that are either heterozygous or homozygous alternative.
Some indels that were originally discovered were found to be the homozygous reference genotype. Invariably, these are relative high depth calls where the
Some indels that were originally discovered were found to be the homozygous reference genotype. Invariably, these are relative high depth calls where the
alternative allele is discovered less or is mis-specified.
alternative allele is discovered less or is mis-specified.
