User: naruto1nrt

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naruto1nrt20
Reputation:
20
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New User
Location:
Australia
Last seen:
1 year, 4 months ago
Joined:
3 years, 2 months ago
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n*********@gmail.com

Posts by naruto1nrt

<prev • 10 results • page 1 of 1 • next >
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How does GATK caculate the HaplotypeScore in Unified Genotyper
... I have a snp with HaplotypeScore=14 which must be filtered by hard filter(HaplotypeScore>13).But I am sure about this snp is true. So do anybody know how does GATK caculate the HaplotypeScore in Unified Genotyper? thanks ...
software error gatk unified genotyper next-gen snp written 20 months ago by naruto1nrt20
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Answer: A: Problem with alignment
... In your command, file3 and file4 will be ignore. Your bam file didn't have these reads! ...
written 2.8 years ago by naruto1nrt20
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Can construct NJ tree with normal samples besd on somatic snvs?
... in somatic mutation dataset, info about normal samples will be 0.SO how can i construct evolution tree using somatic snvs with normal samples in? Do anyone have some suggestions?  ...
genome snp sequencing written 2.9 years ago by naruto1nrt20
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Answer: A: Genome Music - Calc-Bmr
... i meet that error too: Use of uninitialized value within %gene_idx in array element at /PUBLIC/software/HEALTH/04lib/perl/lib/perl5/site_perl/5.18.2/Genome/Model/Tools/Music/Bmr/CalcBmr.pm line 295, <GEN25> line 20312. Use of uninitialized value within %gene_idx in array element at /PUBLIC/so ...
written 3.0 years ago by naruto1nrt20
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databases depended by MuSic
... Should I by myself download the databases,cosmic and pfam for example, or these will be downloaded when install? ...
genome written 3.1 years ago by naruto1nrt20
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Why muTect Error?
... When I use muTect to call somatic SNVs, i got this error: INFO  10:05:12,111 ProgressMeter -       1:1249156        3.86e+05   51.1 s        2.2 m      0.1%        12.7 h    12.7 h  INFO  10:05:13,434 MuTect - [MUTECTOR] Processed 21006455 reads in 23342 ms  INFO  10:05:14,428 MuTect - [MUTECTOR] P ...
software error written 3.1 years ago by naruto1nrt20
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can picard use multiple threads?
... is there an argu can make picard multiple threads? in the picard home page,i didn't find it. ...
alignment written 3.1 years ago by naruto1nrt20 • updated 19 months ago by l0o0100
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bwa mem + GATK +mutect
... align with bwa mem realign and BQSR with GATK then got the final bam but when I use muTect to call somatic snv,I got an error.   command: java -Xmx2g -jar muTect.jar \        --analysis_type MuTect \        --reference_sequence human_g1k_v37_decoy.fasta        --cosmic b37_cosmic_v54_120711 ...
software error alignment written 3.2 years ago by naruto1nrt20 • updated 9 days ago by Biostar ♦♦ 20
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Is there an software can handle CNV analysis without control for WES data?
... Does control-freec can handle it? I found it in a paper? but when using it,i got this error: ERROR: Currently you need to provide a control sample ('mateFile' or 'mateCopyNumberFile') when you analyze targeted sequencing data to eliminate capture bias. The GC-content bias is not the only bias in ...
software error written 3.2 years ago by naruto1nrt20 • updated 3.2 years ago by poisonAlien2.4k
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the bam file generated by bwa mem mode don't have SM tag?
... I start to use mem mode recently,but when i found it not have SM tag in bam file. is there any parameter for this? ...
alignment written 3.2 years ago by naruto1nrt20 • updated 3.2 years ago by Devon Ryan70k

Latest awards to naruto1nrt

Popular Question 2.7 years ago, created a question with more than 1,000 views. For bwa mem + GATK +mutect
Popular Question 2.7 years ago, created a question with more than 1,000 views. For can picard use multiple threads?

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