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cancerit / PCAP-core

NGS reference implementations and helper code for mapping (originally part of ICGC-TCGA-PanCancer)
GNU General Public License v2.0
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bam_stats - qcfail reads #8

Closed keiranmraine closed 6 years ago

keiranmraine commented 6 years ago

Modify to accept qcfail into counts of total reads.

keiranmraine commented 6 years ago

@drjsanger what do you think we should do about these? We are going to start having them at the final BAM level but not at lane level. If we skip them where we do currently we loose some of the duplicate and mapping info, but we also don't capture a count for these.

I'd propose just counting them and adding to the output file as we only apply to reads that would pass the usual set of checks (proper-pair, not dup/supp/non-primary).

Thoughts?

keiranmraine commented 6 years ago

Decision to add a new pair of counts for qcfail read 1/2. Counting in other areas will include these reads.

keiranmraine commented 6 years ago

Done, merged into feature/rg_metadata