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User: lffu_0032

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lffu_0032 • 30
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Posts by lffu_0032

<prev • 11 results • page 1 of 2 • next >
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Comment: C: is DANN capable of scoring insertion and deletion?
... CADD is just for SNP and based the "same feature set and training data used by DANN", i guess that DANN is also just for SNP. "Please note that only SNPs have CADD scores, as indels/CNVs cannot be matched to CADD database." from http://annovar.openbioinformatics.org/en/latest/user-guide/filter/#cad ...
written 3 months ago by lffu_0032 • 30
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Comment: A: is DANN capable of scoring insertion and deletion?
... i have the same question. anyone know detail?thanks for your help！ ...
written 3 months ago by lffu_0032 • 30
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Comment: C: algorithm of gatk re-alignment
... at the first step that i showed above: 1）Finds minimum alternate consensus sequence(s) that best fits reads. i do not know the exact meaning of this sentence. i am going to read the gatk-dev team's nature genetics paper titled "A framework for variation discovery and genotyping using next-generation ...
written 3 months ago by lffu_0032 • 30
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Comment: C: algorithm of gatk re-alignment
... of course i had looked through this two pages carefully, i mean the detail information of re-align. this two pages just give some basic principles of re-align and show some examples about how to use it, plus the detailed meanings of each parameter. however, i really can not find more explanations ab ...
written 3 months ago by lffu_0032 • 30
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Answer: A: Difference in Haplotypecaller in GATKv4 Vs Gatk3.7
... the algorithm of HC between gatk-3.7 and gatk-4.0 is almost same, you can see from: https://gatkforums.broadinstitute.org/gatk/discussion/10925/9-things-youve-been-dying-to-know-about-the-haplotypecaller-paper. Q: How does the methodology compare to GATK4? A: The GATK engine that parses the BA ...
written 3 months ago by lffu_0032 • 30
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algorithm of gatk re-alignment
... hi, everyone, i always have a question about the detailed algorithms used in gatk re-alignment step. i looked through the GATK documents but did not find useful information. the only thing useful i found is in the GATK wrokshop, https://drive.google.com/drive/folders/0BwTg3aXzGxEDN0pTMzV2aGFlQ2M, Re ...
gatk realignment algorithm re-alignment written 3 months ago by lffu_0032 • 30
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Comment: C: Can I install and run igvtools on a server?
... igvtools is not equal with IGV ...
written 3 months ago by lffu_0032 • 30
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Answer: A: Where Can I Get Annovar 'Refgene' Format?
... you can visit http://genome.ucsc.edu/cgi-bin/hgTables and then click "describe the schema" button, the you can see the RefSeq gene predictions format. ...
written 4 months ago by lffu_0032 • 30
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Comment: C: what is the detailed information of .amb .ann .bwt .pac .sa files generated by
... thank you very much. ...
written 8 months ago by lffu_0032 • 30
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Comment: C: Difference Between "Mate Pair" And "Pair-End"
... thanks, it helps a lot ...
written 12 months ago by lffu_0032 • 30

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