User: bluemonster0808

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China
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6 days, 2 hours ago
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Posts by bluemonster0808

<prev • 20 results • page 1 of 2 • next >
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Comment: C: Is my precisionFDA result acceptable?
... Sorry. Because I'm a newbie, I just run a gatk best practice to learn bioinformatics. So I wonder whether this result is good or not? Is this 98.66% meaningful in real NGS scenario? ...
written 18 days ago by bluemonster080830
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Is my precisionFDA result acceptable?
... I ran a WGS analysis of NA12878, and run a comparison on [precisionFDA][1]. I wonder whether the precision of 98.66% is acceptable? ![enter image description here][2] [1]: https://precision.fda.gov/ [2]: http://imageshack.com/a/img924/6085/qBRIrM.png ...
gatk precisionfda written 19 days ago by bluemonster080830 • updated 19 days ago by Michael Dondrup43k
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Comment: C: How about my parallel bwa+gatk pipeline?
... I did split FASTQ files in step 2 "split the 2 fastq files into 8 parts seperately". And then I call 8 "bwa mem" on 8 virutal machines parallelly. "Split bam file and merge bam file" is to generate each chromosome's bam file. ...
written 27 days ago by bluemonster080830
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How about my parallel bwa+gatk pipeline?
... Normally, we run NGS analysis in the follwing steps: 1、 ~/bwa-0.7.16a/bwa mem -t 32 -M -R @RG\tID:1\tPL:Illumina\tSM:HCC1143 ~/reference/human_g1k_v37_decoy.fasta 1.fastq 2.fastq | samblaster --splitterFile my.split.sam --discordantFile my.discord.sam > my.sam 2、 ~/sambamba_v0. ...
gatk ngs parallel pipeline written 27 days ago by bluemonster080830 • updated 27 days ago by JJ80
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Comment: C: GATK HaolotypeCaller takes too much time for variant calling
... sorry , it's my mistake. But I used -nct for HaolotypeCaller , and it runs faster. My command is java -jar GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar -T HaplotypeCaller -R human_g1k_v37_decoy.fasta -I NA12878-Garvan-Vial1.sort.combine.nodup.base_recalibrated.REF_3.bam --genotypin ...
written 28 days ago by bluemonster080830
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Comment: C: GATK HaolotypeCaller takes too much time for variant calling
... Futhermore, you can split the bam file into different chromosomes using "bamtools split -reference" And then call GATK HaplotypeCaller simultaneously on all the chromosomes ...
written 28 days ago by bluemonster080830
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Answer: A: GATK HaolotypeCaller takes too much time for variant calling
... use -nt instead of -nct ...
written 28 days ago by bluemonster080830
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Comment: C: Why the optimal value of BQSR intervals is 20
... This sounds reasonable Thank you! ...
written 4 weeks ago by bluemonster080830
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Comment: C: Why the optimal value of BQSR intervals is 20
... https://ibb.co/cT0if6 you can see the screenshot above I save it on a free image host ...
written 4 weeks ago by bluemonster080830
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Comment: C: What does MT,GL000207 mean?
... ok,i'll pay attention next time ...
written 4 weeks ago by bluemonster080830

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