Mar Gonzàlez-Porta
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Activity overview
Latest activity by Mar Gonzàlez-Porta-
Mar Gonzàlez-Porta commented,
Congratulations on this big milestone! Here a few questions from our team: Does DRAGEN-GATK support low-coverage WGS (5X-1X) / has that been tested? DRAGEN provides a forced genotyping setting to ...
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Mar Gonzàlez-Porta commented,
Hi Brian Wiley, I used different input BAMs for the modeling vs. recalibration steps: (1) run BaseRecalibrator on a subsetted BAM with only autosomes; (2) run ApplyBQSR on the full BAM. Cheers
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Mar Gonzàlez-Porta commented,
Hi Bhanu, Thanks for the response. Please keep us updated on testing outcomes on your end. Since this is such an early step within the analysis pipeline, it has the potential to have a major impact...
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Mar Gonzàlez-Porta commented,
Hi Bhanu, Thanks for the feedback. Here the results of the follow-up analyses that you’ve suggested (slide 4): https://drive.google.com/open?id=1FPu6Fcq1-twjT_1ts2Di0ebizWvDUmBs Labels for items 1 ...
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Mar Gonzàlez-Porta commented,
Hi Bhanu Gandham, Have you had the chance to follow up on this? I wonder if this is a trend specific to our dataset, have you seen a similar behaviour elsewhere? Many thanks,
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Mar Gonzàlez-Porta commented,
Hi Bhanu Gandham, See slide 3 here: https://drive.google.com/open?id=1bun1U9OgNQfD8FQpmR75fWahcMeBFeer In a nutshell, I've re-launched BQSR with the following combinations: Keep input bam as is, b...
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Mar Gonzàlez-Porta created a post,
BQSR returns lower scores for male samples
Hi, We've applied BQSR to our dataset following best practice recipes. When inspecting the results, we've noticed that BQSR returns lower Q scores for male samples (slide 1). We don't see such a sp...