jejacobs23
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Activity overview
Latest activity by jejacobs23-
jejacobs23 commented,
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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jejacobs23 commented,
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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jejacobs23 commented,
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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jejacobs23 commented,
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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jejacobs23 commented,
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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jejacobs23 created a post,
Issues with Java heap space in CollectAllelicCounts
I am using the Copy Number Variation (CNV) tutorial in order to analyze whole genome sequencing samples (along with matched normal controls). When I run the GATK tool, CollectAllelicCounts, I get ...
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jejacobs23 commented,
Thanks sahuno. That worked like a charm.
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jejacobs23 commented,
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...
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jejacobs23 created a post,
Issue with output from CollectAllelicCounts
Hello, I'm using the took CollectAllelicCounts with GATK version 4.1.7.0 and I'm having difficulty with the output file. My code is as follows: REF=<path_to_directory>"/Homo_sapiens_assembly38.fas...
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jejacobs23 created a post,
CollectAllelicCounts interval_list
AnsweredGood afternoon, I am working with GATK 4.1.7.0 and am attempting to use the CollectAllelicCounts function as part of a somatic CNV Workflow. I need some additional help with the interval list that...