Filter VCF file for chr X

Question

[rrapopor]

Hello,

I have RNA-Seq data from hybrid mice b6XCAST, and I'm trying to seperate the data to 2 the allels using Snpsplit. Becuase I have RNA-Seq data, I can't create my own SNP file, therefore I am using the Mouse Genome Project known SNPs list for CAST. The problem is that after runing snpsplit, I get reads in both CAST and b6 X chromosomes for males. I assume there is a problem with the SNP list, or my strains are not very similar to the strains used to create the known list. What filte parmaters should I use on the VCF file, to limited the number of reads mapped to CAST in males?

Thank you