mehar
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Recent activity by mehar Sort by recent activity-
CombineGVCFs suceeded on chrY after 3 days but chrX didn't. I did run GenomicsDBImport on chrX now. This is also weird, it is showing the same log since 56hrs. Very strange :( $ java -versionopenjd...
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Hi Laura, I have provided the centromere and telomere regions to exclude. However, it does not seem to have any impact. Job without excluding telomeres/centromeres running since 28hrs: $ tail array...
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"When I say we don't have best practices for X and Y, that is to say that we don't have any recommendations for how to treat them differently." I understand that, sorry for the nasty comment :) " A...
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It seems to be updating, but very slow. It never had issues on autosomal chromosomes on the same cluster. Assuming the job might be hung, it was re-run 3-4 times already but same behaviour. Below i...
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Below are the HC and CombineGVCF commands shown for chrX. For chrY, chrX is replaced with chrY in the commands. HaplotypeCaller command: $gatk4 --java-options "-Xms10G -Xmx32G -Djava.io.tmpdir=./tm...
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I am running HaplotypeCaller andCombineGVCFs on X and Y separately with the commands shown above. I have used -ploidy 2 on chrX and chrY which is also the default with HaplotypeCaller. "We don't ha...
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It is from a different sample.
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HOw about the other error in the original question `ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE` Is it also from LeftAlignIndels?
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Here it is,--ADD_MATE_CIGAR is set to TRUE. And still the error: Using GATK jar /gatk-4.1.9.0/gatk-package-4.1.9.0-local.jarRunning: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_a...
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So here is more traceback info. Here is the workflow used to trace the issue: Bwa mem -> MergeSam-> FixMateInformation -> SetNmMdAndUqTags -> MarkDuplicates -> SortSam -> FixMateInformation -> Set...