User: bluemonster0808

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Posts by bluemonster0808

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Comment: C: What does MT,GL000207 mean?
... Thank you for your answer~ ...
written 7 days ago by bluemonster08080
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What does MT,GL000207 mean?
... I know human have 1~22 + X/Y chromosomes. But I find MT, GL000207,GL000203 etc in human_g1k_v37_decoy.breakpoints.bed. What are these chromosomes? ...
chromosome written 8 days ago by bluemonster08080
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Comment: C: How to speed up bwa mem?
... 200GB*2 is plain fastq, not compressed. thank you for your answer, I'll try to split it, and figure out the timecost ^_^ ...
written 6 weeks ago by bluemonster08080
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Comment: C: Why the optimal value of BQSR intervals is 20
... Thank you for your reply. As a newbie, I find the GATK Best Practices recommends people to do BQSR in https://software.broadinstitute.org/gatk/best-practices/bp_3step.php?case=GermShortWGS ...
written 6 weeks ago by bluemonster08080
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How to speed up bwa mem?
... I have 2 pair-end fastq files, the size is 200GB * 2. Doing "bwa mem" cost me nearly 6 hours on a pretty good machine(24 physical core E5-2670 v3, Hyper-Threading, 64GB memory). There is some problem with the "-t" param . The timecost of "-t 48" and "-t 12" are nearly the same. I wonder if it's ...
wgs bwa written 6 weeks ago by bluemonster08080 • updated 6 weeks ago by Brian Bushnell14k
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Comment: C: Why the optimal value of BQSR intervals is 20
... Here is my command with -L 20 java -Xmx50000M -jar GenomeAnalysisTK-3.5-0-g36282e4/GenomeAnalysisTK.jar --analysis_type BaseRecalibrator -nct 48 --out CCLE-HCC1143-DNA-10_Illumina.converted.sorted.deduped.recal_L20data.grp --disable_indel_quals --reference_sequence human_g1k_v37_decoy.fasta --in ...
written 7 weeks ago by bluemonster08080
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Why the optimal value of BQSR intervals is 20
... I see a hint in SevenBridges "BQSR intervals optimal value is 20 or chr20 *". I tried running GATK BaseRecalibrator with and without -L 20, the result files are nearly the same. Why? We don't need to do BQSR in chromosomes other than chr20? ...
wgs gatk written 7 weeks ago by bluemonster08080
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Comment: C: Why people use gatk v2.3.9lite?
... Thany you for your answer I send an e-mail to Seven Bridges' support team, but two days passed and no reply.... ...
written 9 weeks ago by bluemonster08080
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Why people use gatk v2.3.9lite?
... In seven bridges, I only find gatk v2.3.9lite and gatk4. Why there isn't gatk3.x? Why people mainly use v2.3.9lite? ...
gatk written 9 weeks ago by bluemonster08080 • updated 9 weeks ago by h.mon9.0k

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