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BQSR with intervals & cut-off base coverage or interval average coverage

manolismanolis Member ✭✭
edited May 2018 in Ask the GATK team

GATK4.0.4.0, scattering


if I'm correct:

when I process in the BQSR an interval with very low coverage (0x - 3x base coverage), then I have the error "RecalibrationReport - Missing read group(s) ..." if I go forward to the HaplotypeCaller I have a new error "USER ERROR ... Interval/contig... loci" ...

When the coverage is high everything is ok.

If the above "relation" between errors and steps is correct... what happen when I have two target regions inside an interval, one with a high coverage and the other one with a very low coverage? I lose both regions data or only of the not well covered?

What is the cut-off of reads/coverage/base coverage of BQSR, or average coverage of the inteval?

Many thanks


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