Holiday Notice:
The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!

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

Hi,

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

Answers

Sign In or Register to comment.