Hello,everybody!
I've got a file named "chr12.map" by Maq,then I convert it to "chr12.sam" by samtools.Finally,I use pileup to obtain the SNP file:"chr12.final.plp".
Comparing the two files,I find that there are many postions in "chr12.final.plp",but not in "chr12.map".Why?
I've got a file named "chr12.map" by Maq,then I convert it to "chr12.sam" by samtools.Finally,I use pileup to obtain the SNP file:"chr12.final.plp".
Comparing the two files,I find that there are many postions in "chr12.final.plp",but not in "chr12.map".Why?