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gt1 / biobambam2

Tools for early stage alignment file processing
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bammarkduplicates - unusual case #78

Closed keiranmraine closed 5 years ago

keiranmraine commented 5 years ago

Hi,

We have an additional QC phase on our mapped data where we mark single reads from a pair as QCFAIL but they remain properly-paired.

Unfortunately when these reach bammarkduplicates they are not processed as either single end mappings or pairs and we end up with PCR duplicates.

Is there any possibility this could be handled as either a single end mapping?

Thanks, Keiran

keiranmraine commented 5 years ago

Additional info. It appears that samtools markdup handles these as single-end mappings

keiranmraine commented 5 years ago

We've found an alternative solution for this