jejacobs23
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Recent activity by jejacobs23 Sort by recent activity-
Thanks for your patience Genevieve. As for your questions, the DepthOfCoverage never did finish and the .vcf file did not have any unusually long lines in it. I went ahead and tried a few differe...
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I'm not sure I understand what you mean. I'm running GATK DepthOfCoverage on my input .bam file, not the .vcf file.
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Thanks again Genevieve for all your help with this issue. I'm running the DepthofCoverage tool but as of yet, it hasn't finished (>24 hours). As for converting the .vcf.gz into and Picard-style i...
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Thank you so much Genevieve. Here is some additional information: The SNPs-only file used in the "-L" option is a .vcf.gz file and is 2.5Gb The .bam file is 177Gb
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Thank you Genevieve. I converted the CRAM input to a BAM and created an index file (using Samtools). Unfortunately, I'm still getting the same error with the java heap space running out of memory...
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Thanks sahuno. That worked like a charm.
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Thank you sahuno, Elizabeth237 and Genevieve for your comments on this issue. I'm still having the same problem with accessing the file from the GATK Resource Bundle. As stated in my original pos...