User: dare_devil
dare_devil • 1.3k
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Posts by dare_devil
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... `--max-gaussians` default value is 8. I have changed to `6` for that particular sample ...
written 3 days ago by
dare_devil • 1.3k
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I performed variant reclibration on 15 `vcf` files. But 1 vcf file encountered user error as follows:
A USER ERROR has occurred: Positive training model failed to converge. One or more annotations (usually MQ) may have insufficient variance. Please consider lowering the maximum number of Gau ...
written 3 days ago by
dare_devil • 1.3k
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... What have you done before aligning the reads to the reference genome? ...
written 3 days ago by
dare_devil • 1.3k
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... for plotting you can consider `z score` where as if you want to look at differentially expressed genes you may take `normalized` data ...
written 4 days ago by
dare_devil • 1.3k
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... Update: When I executed your code one by one it started running. But When I saved your code in a file as `parallel_haplo.sh` it does not work.
`sh parallel_haplo.sh`
It gives the error:
`parallel_haplo.sh : 6: export: Illegal option -f`
It works when I run as `bash parallel_haplo.sh`. I don't know ...
written 5 days ago by
dare_devil • 1.3k
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... Ya I have taken the same code provided by you. It gives an error `export: Illegal option -f` ...
written 5 days ago by
dare_devil • 1.3k
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... The answer given by [Malcolm.Cook][1], [ole.tange][2] and [cpad0112][3] works well
Method 1:
parallel gatk --java-options "-Xmx40g" HaplotypeCaller \
-R /media/gatk/Homo_sapiens_assembly38.fasta -I {} -O {.}.vcf.gz \
--dbsnp /media/gatk/dbsnp_138.hg38.vcf.gz \
-L /media/gatk/tar ...
written 5 days ago by
dare_devil • 1.3k
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128
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... Cheers !! this works!! ...
written 5 days ago by
dare_devil • 1.3k
0
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128
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... This gives me an error `export: Illegal option -f` ...
written 5 days ago by
dare_devil • 1.3k
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2.3k
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Comment:
C: permission denied error
... add this in `.bashrc` file
`export PATH=$PATH:"/media/C2F8EFBFF8EFAFB9/bedops-2.14.2/"` ...
written 5 days ago by
dare_devil • 1.3k
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