I have sequenced many sequences and would like to identify SNPs that are fixed in the population. Which software could I used to call such SNPs (i.e. , SNPs that are different from the reference sequence in all reads)? Thanks.
What you're looking to do is fairly straightforward. I'd just call SNPs with Samtools, then merge the lists with a little script.
From that look of it, what you are trying to do is the standard SNP calling procedure. You might want to try out the bwa -> GATK pipeline where you can find: https://www.broadinstitute.org/gatk/
Once you've got the vcf, it will be easy to obtain the information you want (something like homozygous variation on the sample)
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version 2.3.6
Are you trying to match the SNPs to reference sequences and show only the non-matching ones? Sorry, but I do not fully understand your question.