segmentFst.md

% SEGMENTFST(1) segmentFst (vcflib) | segmentFst (VCF statistics) % Erik Garrison and vcflib contributors

NAME

segmentFst

SYNOPSIS

segmentFst -s 0.7 -f wcFst.output.txt

DESCRIPTION

segmentFst creates genomic segments (bed file) for regions with high wcFst

OPTIONS

**segmentFst** provides a way to find continious regions with high Fst values.  It takes the output of wcFst and produces a BED file.  These high Fst region can be permutated with 'permuteGPATwindow'
Output : 8 columns :                 
     1. Seqid                        
     2. Start (zero based)           
     3. End   (zero based)           
     4. Average Fst                  
     5. Average high Fst (Fst > -s)  
     6. N Fst values in segment      
     7. N high fst values in segment 
     8. Segment length               
required: -f            -- Output from wcFst     
optional: -s            -- High Fst cutoff [0.8] 

Type: statistics

EXIT VALUES

0 : Success

not 0 : Failure

SEE ALSO

vcflib(1)

OTHER

Source code

segmentFst.cpp

LICENSE

Copyright 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed. Copyright 2020-2024 (C) Pjotr Prins.