whether to remove duplicate reads

[chengwenxuan1997]

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?

[tlesluyes]

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.