FilterTable.py filters positions of a input table according to specific annotations indexed by tabix tool. Filtered out positions will be marked with “#†at the beginning of each line. To exclude such lines the option -E should be used. Features are the same as indicated in the third field of GTF annotation file.
FilterTable.py -i mytable -s dbsnp137.gtf.gz -S snp -o mytable_filtered -E -p
Options:
-i Table file
-f Sorted file with positions to filter in (GTF sorted file as above)
-s Sorted file with positions to filter out (GTF sorted file as above)
-F Features to filter in (separated by comma)
-S Features to filter out (separated by comma)
-E Exclude positions filtered out
-o Save filtered lines to a file [stdout]
-p Print simple statistics
-h Print the help