资 源 简 介
This quick and dirty script takes as input a BSNP SNP file and a BED file of intervals and outputs a FASTA file containing sequences for each of those intervals.
Information on BSNP-to-FASTA-via-BED.pl
Quick Start Instructions
To start you need a BSNP file (*.bsnp.snp.out) generated with the BSNP Bayesian SNP caller program:
#ChrName ChrPos RefCall MAQcall #BSNPcall MAQcallQ MAQsnpQ MAQrmsQ P(Data)_NLL10...chr1 22905 C C C 30 0 60 6.0206e-01...chr1 22906 T T T 30 0 60 6.0206e-01...chr1 22907 C C C 30 0 60 6.0206e-01...chr1 22908 T T T 30 0 60 6.0206e-01...chr1 22909 G G G 30 0 60 6.0206e-01...chr1 22910 C C C 30 0 60 6.0206e-01...[...]
And a BED file of genomic intervals you"d like to pull out:
chr1 626660 627450chr1 1047725 1048248chr1 1315209 1315762chr1 1318438 1319013[...]
Running the Perl
