Dear experts,
I have used GATK to Base quality score recalibration. After TableRecalibration, it will rewrite the quality scores (in the QUAL field) using the data in the recal_data.csv file, into a new BAM file.
After I got the bam file, should I remapping the bam file using BWA? This is not indicated by GATK. But I just think if we really get more accurate base quality, remapping the reads will be helpful for the mapping also.
Thank you very much.
I have used GATK to Base quality score recalibration. After TableRecalibration, it will rewrite the quality scores (in the QUAL field) using the data in the recal_data.csv file, into a new BAM file.
After I got the bam file, should I remapping the bam file using BWA? This is not indicated by GATK. But I just think if we really get more accurate base quality, remapping the reads will be helpful for the mapping also.
Thank you very much.
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