Snp130-Masked Fasta Files And Alignment

Question

[Rok]

Hello!

I have some Chip-Seq reads that need aligning, because I want to eliminate bias towards reference alleles I wanted to try aligning with SNP-masked genome.

I have downloaded SNP-Masked sequence files from the UCSC database (http://hgdownload.cse.ucsc.edu/goldenPath/hg18/snp130Mask/), and have tried doing alignment with Bowtie. The problem is that Bowtie gives a mismatch between R (which is G or A) and G.

Is there any other software that works with SNP-masked sequences?

best wishes