Hi,
I am using pysam to identify variants in our data. I was under the impression that the pysam IteratorSNPCall and SNPCaller both use samtools to identify snps. However when I just run Samtools mpileup to identify snps the output that I get is different
Different in the sense that samtools is calling a lot more positions as potential variants as compared to pysam.
Firstly, does pysam actually use samtools for SNP calling and if yes, then why would the outputs be different?
I would really appreciate if somebody could clarify this.
Thanks,
Praful
I am using pysam to identify variants in our data. I was under the impression that the pysam IteratorSNPCall and SNPCaller both use samtools to identify snps. However when I just run Samtools mpileup to identify snps the output that I get is different
Different in the sense that samtools is calling a lot more positions as potential variants as compared to pysam.
Firstly, does pysam actually use samtools for SNP calling and if yes, then why would the outputs be different?
I would really appreciate if somebody could clarify this.
Thanks,
Praful