Open haogecat opened 8 months ago
You don't say how many reads were indicated by either pysam or IGV.
Pysam's pileup()
uses the same machinery as samtools. (So you may also wish to experiment with samtools and its similar parameters.) Usually lower depth than expected is caused by things like max_depth
and min_base_quality
, so you should start by adjusting those arguments.
You don't say how many reads were indicated by either pysam or IGV.
Pysam's
pileup()
uses the same machinery as samtools. (So you may also wish to experiment with samtools and its similar parameters.) Usually lower depth than expected is caused by things likemax_depth
andmin_base_quality
, so you should start by adjusting those arguments.
Thank you very much for your answer, I will try
I used pysam to output the SNPS at locus 22218574 of the reference genome, but the output reads were fewer than what I visualized with IGV. The results of pysam were many fewer reads. Why? Here is the code:
Below is a visualization of igv at site 22218574。![image](https://github.com/pysam-developers/pysam/assets/115456502/0627d89d-5614-4cd1-a4d7-172b65ae5b43)
Sincerely request you, thanks!