Tiffany Kosch
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Activity overview
Latest activity by Tiffany Kosch-
Tiffany Kosch commented,
Hello SkyWarrior, I've tried this but cannot index the file with bai because the chromosomes are too large. Is there another way around this?
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Tiffany Kosch created a post,
HaplotypeCaller java.lang.ArrayIndexOutOfBoundsException: Index 32770 out of bounds for length 32770
REQUIRED for all errors and issues: a) GATK version used: b) Exact command used: c) Entire program log: I keep getting this error when running gatk HaplotypeCaller after it's been running for 6-7 ...
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Tiffany Kosch commented,
Hello Chris Kachulis, Thanks very much for your response and for answering my question about chromosome size limits. I just ran a test with a newer version of Picard and it started up great so I t...
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Tiffany Kosch created a post,
Question about bam format errors and handling large contigs
REQUIRED for all errors and issues: a) GATK version used: gatk/4.1.4.1; picard/2.6.0; samtools/1.12; bwa/0.7.17 b) Exact command used: bwa mem -t 12 -R ${RG} ${REF} ${R1} ${R2} | samtools sort -o ...