NGS BSA simple commands.
FSI2.pl is written by Perl for filtering the SNP-Index form VCF file which made by VarScan or any other SNP/Indel calling softwares.
Get filtered SNP/Indels simple but most important values and get the absolute value of delte SNP-Index.
Usage:
perl FSI2.pl [options] <inputVCFfile>
OR
./FSI2.pl [options] <inputVCFfile>
Output file could be used for next window slide analysis or draw plots of SNP-Index.
Options:
[-o outprefix default: filtered.out]
[-d int|mindepth default: 20]
[-f float|compared samples at least one SNP-index bigger than filterpercent [0-1.0] default: 0.3]
[-n int|number of all samples default: 2]
[-c1 int|The first sample used for comparing to the sencond sample to calculate abs delta SNP-Index default: 1]
[-c2 int|The second sample used for comparing to the first sample to calculate abs delta SNP-Index default: 2]
WSAcount (Window Slide Analysis SNP/Indel Count simple command) is written by Perl for counting the filtered SNP-Index form FSI output file .
Usage:
perl WSAcount.pl [options] -l <Chromesome Length List> <inputFSIout>
Options:
[-o outprefix default: filtered.wsa.out]
[-s int|Step size default:25000]
[-w int|window size default: 50000]
[-f float|ABS delta SNP-Index Filter line [0-1.0] default: -1]
Note: Window slide analysis SNP/Indel counts.