My SNP data is from Sanger sequencing. Multiple samples cover varied regions, not necessary the same fragments. I performed alignment via bwasw and pileup via samtools.
What would be the differences between
1. pileup multiple samples all together
2. pileup one sample at a time?
Also, would QUAL score, DP, AC be affected dramatically?
What would be the differences between
1. pileup multiple samples all together
2. pileup one sample at a time?
Also, would QUAL score, DP, AC be affected dramatically?
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