Hi all,
I'm calling somatic SNVs with the matched tumor/normal-pairs, and the called candidates overlapped among multiple callers were further visualized with the IGV and analyzed manually.
Theoretically, the vast majority of true positive SNVs sould be singletons within a window of 100 bp. However, I found several adjacent high quality candidates were not singletons and emanated from the same reads or read-pairs. I was confused by this kind of adjacent SNVs.
What can explain this kind of high quality non-singleton SNVs ?
I don't know if they were false positives resulted from mapping/aligment errors.
At the preprocessing stage, I removed reads containing Ns, trimmed adaptors and low quality bases (Q30). Then, only paired reads were used and aligned to ref with bwa default settings. When calling SNVs, only reads with mapping quality score > 30 (MAPQ>30) were counted, and threshold for calling an SNV was alternate reads >= 3.
Best regards.
I'm calling somatic SNVs with the matched tumor/normal-pairs, and the called candidates overlapped among multiple callers were further visualized with the IGV and analyzed manually.
Theoretically, the vast majority of true positive SNVs sould be singletons within a window of 100 bp. However, I found several adjacent high quality candidates were not singletons and emanated from the same reads or read-pairs. I was confused by this kind of adjacent SNVs.
What can explain this kind of high quality non-singleton SNVs ?
I don't know if they were false positives resulted from mapping/aligment errors.
At the preprocessing stage, I removed reads containing Ns, trimmed adaptors and low quality bases (Q30). Then, only paired reads were used and aligned to ref with bwa default settings. When calling SNVs, only reads with mapping quality score > 30 (MAPQ>30) were counted, and threshold for calling an SNV was alternate reads >= 3.
Best regards.
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