Page Comparison

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login1$ freebayes --min-alternate-total 23 --ploidy 100 --pooled --vcf SRR032374.vcf \
        --fasta-reference NC_012967.1.fasta SRR032374.sorted.bam

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• Write a script or use a linux command to filter the output files to only contain variants that are predicted to have frequencies > 0.05 10 and < 0.90 or scores > 1000100.
• What does the --min-alternate-total option mean. Experiment with using other options and examine how they affect speed versus what is predicted. Beware that some choices of options can cause crashes.

Run deepSNV

deepSNV runs more slowly, so we will only look at a small region of the genome initially in interactive mode. (Why is it slower? Probably in part due to using a more sophisticated statistical model and in part because it is implemented in R instead of C.)

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