mehar
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Latest activity by mehar-
mehar commented,
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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mehar commented,
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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mehar commented,
"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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mehar commented,
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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mehar commented,
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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mehar commented,
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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mehar created a post,
CombineGVCF on chrX and chrY hg38 running for ever
I have been running HaplotypeCaller (HC) on 25 WGS samples on hg38 aligned BAM files. HC was run on the entire genome including autosomes and sex chromosomes in two different ways 1) HC on each chr...
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mehar commented,
It is from a different sample.
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mehar commented,
HOw about the other error in the original question `ERROR::MATE_CIGAR_STRING_INVALID_PRESENCE` Is it also from LeftAlignIndels?
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mehar commented,
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...