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niu-lab / msisensor2

Microsatellite instability (MSI) detection for tumor only data.
GNU General Public License v3.0
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Does msisensor2 requires duplicate marked basequality recalibrated BAM or the raw BAM? #13

Open vlakhujani opened 4 years ago

vlakhujani commented 4 years ago

Hi

I have a question about the input BAM file to be used for msisensor2 program.

Does msisensor2 requires duplicate marked BAM OR duplicate marked + basequality recalibrated BAM or the raw BAM?

owehann commented 4 years ago

Hi In fact, this is determined by the sequencing depth. If it is relatively high, I will suggest a necessary dedup step. According to the feedback from other companies, if the sequencing process takes place on an Illumina sequencer with flowcell as its basic unit, there is little difference between dedup or not dedup when the sequencing depth is less than 1000X.

vlakhujani commented 4 years ago

@owehann thanks for the response. How about base quality re calibration ? Do I need to perform that?

SouzaBB commented 3 years ago

@owehann thanks for the response. How about base quality re calibration ? Do I need to perform that?

Are you using BQSR? Have you noticed any difference between using it and not using it?