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RG PL field value is not spec compliant #46

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jkbonfield opened this issue Oct 24, 2022 · 0 comments
Open

RG PL field value is not spec compliant #46

jkbonfield opened this issue Oct 24, 2022 · 0 comments

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@jkbonfield
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The SAM header @RG sub field "PL" is listed as PL0 at

os << "@RG\tID:" << rgid << "\tLB:LB0\tPL:PL0\tPU:PU0\tSM:" << rgsm << "\n";

This is being reported by users as turning up in data, which will cause problems for any data which validates the input matches the specifications. The default from DRAGMAP should be ILLUMINA. This field is a controlled vocabulary, designed to allow users to tune their algorithms to the type of data being generated. The PM field (Platform Model) is more flexible and permits additional machine details.

Reported via samtools/hts-specs#679

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