Alex van Vliet
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Activity overview
Latest activity by Alex van Vliet-
Alex van Vliet commented,
Hi! Is it recommended to use GenomicsDBImport for WES data? Should I provide an intervals file that is essentially the target .bed?
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Alex van Vliet commented,
Hi Anthony, I ended up solving this by figuring out my fastq was not interleaved. I have no idea how this happened for one file, I suspect it had something to do with an abrupt Snakemake stop and i...
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Alex van Vliet commented,
I'm thinking maybe there is a problem with bwa-- I started getting an additional error: java.lang.IllegalStateException: Aligned record iterator (HS31_27052:1:1101:10000:11450) is behind the unmapp...
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Alex van Vliet created a post,
mergeBamAlignment error: inappropriate call if not paired read
REQUIRED for all errors and issues: a) GATK version used: 4.2.2.0b) Exact command used: /DATA/peeper_lab/gatk/gatk --java-options '-Xmx16G -XX:ParallelGCThreads=4' MergeBamAlignment R=/DATA/peeper_...