Can bams with marked duplicates(without removing) be used as input for snp-pileup?

mskcc / facets

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.

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Can bams with marked duplicates(without removing) be used as input for snp-pileup? #197

Closed THT-sleepy closed 5 months ago

THT-sleepy commented 8 months ago

Hello!

I'm wondering if bams with marked duplicates(without removing) can be used as input for snp-pileup?

I noticed that in issue #148 you mentioned that bams should be deduplicated before using as input, however, I don't know if it is ok to use bams whose duplicates were marked by Picard-Markduplicates instead of removing as input for snp-pileup.

Thank you!

Best Tang