I am working on a project to identify and genotype SNPs in targeted genes. I
did some analysis using Galaxy. First, mapping to the genome with Bowtie.
Second, identify SNPs using MPileup in SAMtools. When I got the pileup file,
the SNP information is in which chromosome and what position. I would like
to focus on the SNPs within genes. How could I extract the SNP information
for each genes (SNP position, coverage)? Is there a tool in Galaxy to
fulfill this? Any help is highly appreciated!
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