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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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Hotfix/4.3.1 #38

Closed ghost closed 5 years ago

ghost commented 5 years ago

@keiranmraine Please comment

keiranmraine commented 5 years ago

@drjsanger Has this been run over a BAM/CRAM file and confirmed to work as expected?

ghost commented 5 years ago 
$ install/bin/mismatchQc -i /path/to/input.bam -p | samtools-1.3.1 view -H | grep -e '^@PG'

Results in:

...

@PG ID:PCAP-core-mismatchQC.1   PN:PCAP-core-mismatchQC PP:bammerge'    CL:install/bin/mismatchQc -p -i /path/to/input.bam -o - DS:Marks a read as QCFAIL and adds aux tag 'mm' where the mismatch rate higher than the threshold   VN:4.3.1

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