zhaol
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Activity overview
Latest activity by zhaol-
zhaol commented,
Hi, Bhanu Gandham. First, I fixed BAM with the FixmateInformation program.After I fix BAM, I re-run the ValidatArray and ValidatesSamFile and no error messages are displayed. Second, I need to reco...
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zhaol created a post,
ASEReadCounter java.lang.ArrayIndexOutOfBoundsException: 0
When I ran AsereadCounter, BAM generated from RNA-seq and VCF generated from RNA-seq, but the error occurred. java.lang.ArrayIndexOutOfBoundsException: 0 Then I ran validateSamFile and vlidateViant...
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zhaol commented,
Hi, Genevieve Brandt. I re-generate the indexes for all of the vcf.gz files that are input to VariantRecalibrator and the issue has been solved. Thank you and the developer very much.
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zhaol commented,
Hi Genevieve Brandt, the output is too long for this comment. So I choose a part of output-file and paste here. For my vcf.gz created by HaplotypeCaller: Block #742905 at file offset 9660186303- co...
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zhaol commented,
Yes, I first delete the old index files and then reindex with IndexFeatureFile. But as I mentioned above, the error remains.
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zhaol commented,
I don't know if this information is helpful to you. I directly ran VQSR with the VCF outputed by HaplotypeCaller, and no errors occurred. So, I guess the error happened because of GenotypeGVCFs? An...
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zhaol commented,
Hi Genevieve Brandt! When I rerun this workflow, I encountered a similar error --htsjdk.samtools.SAMFormatException: Invalid GZIP header(still occur when running VariantRecalibrator). I remember I ...
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zhaol commented,
Hi, Genevieve Brandt. Thank you for your help. I just solved the error. As you mentioned above, I have some problems with my index because I use tabix to index my VCF files from the HaplotypeCaller...
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zhaol commented,
when I run ValidateVariants with both the zipped and unzipped versions, the result both are A USER ERROR has occurred: Input f1.hc.g.vcf.genotyped.gz fails strict validation of type ALL: one or mor...
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zhaol commented,
Using GATK jar /home/zhaol/biosoft/gatk-4.1.8.0/gatk-package-4.1.8.0-local.jarRunning:java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_...