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Simple program to cap mapping quality in a given alignment file

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capmq

Cap the mapping quality in a given alignment file.

One way to deal with low level contamination in your alignment files is to cap the mapping quality at some level that reflects your estimated certainty that your reads do indeed come from your sample. If you esimate your level of "contamination" (e.g. via a program like VerifyBamID) at, say 10^-3, then your cannot say with more certainty than MAPQ=30 that your reads are mapped correctly:

capmq -C30 in.bam

capmq uses htslib for SAM/BAM/CRAM reading and writing.

git clone git://github.com/mcshane/capmq.git
cd capmq
make HTSDIR=/path/to/your/htslib/install/or/build/dir
make test

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Simple program to cap mapping quality in a given alignment file

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