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Semen Leyn

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Latest activity by Semen Leyn
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    Semen Leyn commented,

    Thank you, now I understand the issue much better. However it complicates some filters as you can't tell where MBQ20 came from - from low base quality or PCR error adjustments.

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    Semen Leyn created a post,

    Mutect2 overlapping reads behavior with --pcr-snv-qual parameter

    Hello! Could you help me understand how does the "--pcr-snv-qual" parameter work? I have a dataset with 150nt paired reads with most of quality scores equal 37. However based on bam file QC almost ...

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    Semen Leyn commented,

    That was my thought. Thanks!

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    Semen Leyn created a post,

    BI and BD tags.

    Hi! I'm using LoFreq software for variant calling and as the preprocessing step I'm using BaseRecalibrator/ApplyBQSR. Recently after I've updated to version 4.1.4.1 (previous was 3.5). I found that...