Brainstorming

necessary subroutines

sync2

• bam2sync (multiple bams and readgroups)
• subsample
• simplesnp
• vcfsnp (use results from external SNP caller in vcf format)
  *

pop1

• compute-measure --samples 1,3,5,7,8 --measure TDc,TD,Pi,WuD,etc (will compute every requested measure for every requested sample), separate routine for windows and snps?

pop2

• fst --pairs 1-2,3-4,5-6 etc (will only compute for the requested pairs, --min count may only apply for each pair)
• fet --pairs 1-2,3-4,5-6
• cmh --comp 1-2,3-4

user suggestions

J.E.

You reccomend using the Bonferroni correction to take the threshold for
significantly different SNPs or genes.
However there are now many papers suggestiong that this is too
conservative and they recommend using the Experimentalwise Error

[Arijit Ghosh]

Hi, I do not see any codes here?