Closed chengwenxuan1997 closed 1 year ago
Hi @chengwenxuan1997,
To process HTS data, ASCAT uses alleleCounter which (in our setting) only considers high-quality reads (base qual >= 20, mapping quality >= 35), discarding (amongst other SAM flags) PCR duplicates. So it doesn't matter whether duplicated reads have been removed or flagged, they will not be used for allele counting.
Cheers,
Tom.
Thanks for this great tool. But I was confused about which bam should be taken as input. I marked the duplicated reads with Picard. Should I remove these duplicate reads?