How does hisatgenotype handle duplicate reads?

DaehwanKimLab / hisat-genotype

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How does hisatgenotype handle duplicate reads? #75

Open yingchen69 opened 1 year ago

yingchen69 commented 1 year ago

Hi,

I have a question regarding duplicate reads. How does hisatgenotype handle duplicate reads? Dose it remove duplicate reads or it's up to user to remove?

I started with the same gatk pre-processed bam file and got totally different results depending on whether I removed the duplicate reads first or not.

Thanks,

Ying