Ryan Welch
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Activity overview
Latest activity by Ryan Welch-
Ryan Welch commented,
That helped a lot. It takes about 12 hours now. Thank you, Ryan
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Ryan Welch commented,
Hello! I will try that and post on here once it is finished.
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Ryan Welch created a post,
BaseRecalibrator on GATK 4.5 Takes multiple days for a sample
REQUIRED for all errors and issues: a) GATK version used: 4.5b) Exact command used: gatk BaseRecalibrator -I /data/BI_data/nbs/aligned_reads/SRR062634_sorted_dedup_reads.bam -R /data/BI_data/nbs/hg...
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Ryan Welch commented,
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 commented,
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 created a post,
gatk4.5 markduplicatesspark error spark
REQUIRED for all errors and issues: a) GATK version used: 4.5b) Exact command used: atk MarkDuplicatesSpark -I /data/BI_data/nbs/aligned_reads/SRR062634.paired.sam -O /data/BI_data/nbs/aligned_read...