User: dare_devil

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dare_devil1.3k
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Posts by dare_devil

<prev • 79 results • page 1 of 8 • next >
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Comment: C: A USER ERROR has occurred: Positive training model failed to converge.
... `--max-gaussians` default value is 8. I have changed to `6` for that particular sample ...
written 3 days ago by dare_devil1.3k
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A USER ERROR has occurred: Positive training model failed to converge.
... 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 ...
vcf gatk max-gaussians written 3 days ago by dare_devil1.3k
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Comment: C: Too many unmapped reads - STAR alignment
... What have you done before aligning the reads to the reference genome? ...
written 3 days ago by dare_devil1.3k
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Comment: C: Should I use Z-score standardization or Min-Max scaling in biological data ?
... 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_devil1.3k
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Comment: C: Is it possible to run haplotypecaller in gnu parallel ?
... 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_devil1.3k
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Comment: C: Is it possible to run haplotypecaller in gnu parallel ?
... Ya I have taken the same code provided by you. It gives an error `export: Illegal option -f` ...
written 5 days ago by dare_devil1.3k
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Answer: A: Is it possible to run haplotypecaller in gnu parallel ?
... 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_devil1.3k
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Comment: C: Is it possible to run haplotypecaller in gnu parallel ?
... Cheers !! this works!! ...
written 5 days ago by dare_devil1.3k
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Comment: C: Is it possible to run haplotypecaller in gnu parallel ?
... This gives me an error `export: Illegal option -f` ...
written 5 days ago by dare_devil1.3k
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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_devil1.3k

Latest awards to dare_devil

Scholar 5 days ago, created an answer that has been accepted. For A: different IDs conversion to Gene ID/symbol
Appreciated 6 days ago, created a post with more than 5 votes. For A: different IDs conversion to Gene ID/symbol
Appreciated 6 days ago, created a post with more than 5 votes. For A: Recalibrating variants in GATK4.1 as compared to GATK3.7
Appreciated 6 days ago, created a post with more than 5 votes. For A: GATK4 VariantRecalibrator resource error
Good Question 6 days ago, asked a question that was upvoted at least 5 times. For Qualimap: java.lang.RuntimeException: The raw data doesn't exist for sample ?
Good Question 6 days ago, asked a question that was upvoted at least 5 times. For How to pipe samtools mileup with varscan trio caller?
Good Question 6 days ago, asked a question that was upvoted at least 5 times. For Calling triovariants using varscan from a compressed mileup file ?
Good Question 6 days ago, asked a question that was upvoted at least 5 times. For How to call denovo and rare variants from a trios cohort?
Good Answer 6 days ago, created an answer that was upvoted at least 5 times. For A: different IDs conversion to Gene ID/symbol
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: different IDs conversion to Gene ID/symbol
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Student 6 days ago, asked a question with at least 3 up-votes. For How to pipe samtools mileup with varscan trio caller?
Appreciated 6 days ago, created a post with more than 5 votes. For A: different IDs conversion to Gene ID/symbol
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