SNP from RNAseq

~/Biosoft/samtools-0.1.6_x86_64-linux/samtools pileup -f ~/GenomeSequence/WholeGenome.fa david_li_bc_transcriptme_07_20_10_bcSample1_F3_bxd_34.bam >david_li_bc_transcriptme_07_20_10_bcSample1_F3_bxd_34.pileup

~/Biosoft/varscan/VarScan.v2.2.jar pileup2snp david_li_bc_transcriptme_07_20_10_bcSample1_F3_bxd_34.pileup >david_li_bc_transcriptme_07_20_10_bcSample1_F3_bxd_34.snp