Changes

* <code>--dbsnp</code>

* <code>--dbsnp</code>

This file has two columns. First column is the chromosome name which must be consistent with the reference created above.

This file has two columns. First column is the chromosome name which must be consistent with the reference created above. Second column is 1-based SNP position. If you want to create your own dbSNP data from downloaded UCSC dbSNP file, one way to do it is: <code>cat dbsnp_129_b36.rod|grep "single" | awk '$4-$3==1' |cut -f2,4 > dbSNP_129_b36.tbl</code>

* <code>--gccontent</code>

* <code>--gccontent</code>