Hello all,
I used samtools to detect indel (aligned by bwa), which identified >1m indels, it's too much comparing with data in publications. Default setting used expect Q50.
The number of indel will drop sharply when RMS>50, the default setting is 10.
Does anyone know how to set the filter to get a reasonable number of indel? How do I know the maxmum length of indel? (bwa sampe does not have such option)
Many thanks!
I used samtools to detect indel (aligned by bwa), which identified >1m indels, it's too much comparing with data in publications. Default setting used expect Q50.
The number of indel will drop sharply when RMS>50, the default setting is 10.
Does anyone know how to set the filter to get a reasonable number of indel? How do I know the maxmum length of indel? (bwa sampe does not have such option)
Many thanks!
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