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3. BaseRecalibrator on GATK 4.5 Takes multiple days for a sample

That helped a lot. It takes about 12 hours now.  Thank you,  Ryan 

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• Ryan Welch
• June 27, 2024 15:46
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1. Community
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3. BaseRecalibrator on GATK 4.5 Takes multiple days for a sample

Hello! I will try that and post on here once it is finished. 

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• Ryan Welch
• June 26, 2024 12:44
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3. gatk4.5 markduplicatesspark error spark

Hello Gökalp Çelik, I ran the follwong command: gatk MarkDuplicatesSpark -I /data/BI_data/nbs/aligned_reads/SRR062634.paired.sam -O /data/BI_data/nbs/aligned_reads/SRR062634_sorted_dedup_reads1.bam...

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• Ryan Welch
• June 25, 2024 20:18
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3. gatk4.5 markduplicatesspark error spark

This is the command: gatk MarkDuplicatesSpark -I /data/BI_data/nbs/aligned_reads/SRR062634.paired.sam -O /data/BI_data/nbs/aligned_reads/SRR062634_sorted_dedup_reads.bam --java-options "-Djava.io.t...

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• Ryan Welch
• June 20, 2024 21:12
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