PAIR2: efficient and powerful software to detect polymorphic Alu elements in high-throughput sequencing data. NB: unpublished yet. Please contact me for usage configFile: indicate the paths of input/output files and parameters to use in the program. @p: denote parameter 'p' given in configFile

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run alu_deletion (make opt3/alu_delete)

 (1) run "alu_delete configFile preprocess"
 	 sort the alu position file, make folders for outputs

 (2) run "alu_delete configFile write_tmps_pn X" 
     X is index of individual according to the @file_pn. eg. for 2000 individuals, we can have 2000 jobs running in parallel, X ranging from 0 to 1999. 
 30X sequencing depth takes about 5hrs per individual (very rarely it may exceed 12 hrs)  

 (3) run "alu_delete configFile write_vcf_pns"
     make big vcf files     

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run alu_insertion (make opt3/alu_insert)

  step(2) takes a few hours to run, all the other steps takes < 60 min, < 4G memory is enough for 99.9% samples.

 (1)  alu_insert configFile preprocess  

 (2)  run "alu_insert configFile write_tmps_pn X", X is index of an individual.

 (3)  make a file, @file_pn_used 
  include a subset of individuals from file @file_pn, individuals failed to run step (2) or with large amount of discordant reads are excluded.
  eg. 2000 individuals, up to 10% can be removed because it takes too much time to handle their discordant reads.

 (4) run "alu_insert configFile combine_pos_pns"
      which generate files named @file_alu_insert1/insert_pos.chr*  

 (5) run "alu_insert configFile clipReads_pn X" for each pn
     write positions of clip reads at @file_alu_insert1/clip/chr*/pn
 X is index of individual, if its corresponding name does not exist in @file_pn_used, the program will quit

 (6) run "alu_insert configFile clipReads_pns chr*" for each chromosome (chr1 - chrX)
 	 write insert_alu1/clip/chr*_pos/*
     which generate files at  insert_alu1/clip/chr*.clip_pn and  insert_alu1/clip/chr*.clip_region

 (7) run "alu_insert configFile write_tmp0_pn X" for each pn
     which writes alu and clip reads for each individual, at insert_alu1/cons/chr*/*

 (8) run "alu_insert configFile clipPos_pns chrX" for each chromosome (chr1 - chrX)
     write exact insertion breakpoints at  insert_alu1/cons/chr*_clip_pass       

 (9) run "alu_insert configFile write_tmp2_pn X" for each pn
     genotype calling      

 (10) run "alu_insert configFile fixed_vcf_pns" 
     final vcf file