I have a sample that has been split and ran in two different machines. For that sample I have reads with two different read groups and in 2 pairs of fastq files. Would be okay to align them separately so I will obtain 2 different bam files, each of the bam files will have the appropriate read group. Would be then possible to pass those 2 bam files to the base quality recalibration tool and then to the haplotypecaller? Otherwise, could you please suggest how to deal with this?
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