User: Tonyzeng

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Tonyzeng300
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5 years, 8 months ago
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Posts by Tonyzeng

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Information Has Missed And Messed After Converting Annotated Whole-Genome Data Into Txt File
... Hey, I am using annovar software to annotate my variants, it works well. HOwever, when I converted annotated variant file into txt file, some of the information have missed for no reason as follows, 1) Annotation of variant file $ annotate_variation.pl --buildver mm10 mysnps.annovar mm10db/ OUT ...
annotation ngs conversion annovar written 5.4 years ago by Tonyzeng300 • updated 5.4 years ago by Alex Paciorkowski3.3k
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Comment: C: The Tools For Reducing Variants
... Sorry for not explaining it clearly. When I used annovar Variants_Reduction tool, for my case for mouse genome. It needs mouse snpdb under annovar database file but Annovar does not provide it. Then i download snpdb from NIBI or Sanger, however, the tools did not recognize it. As for the CombineVa ...
written 5.4 years ago by Tonyzeng300
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The Tools For Reducing Variants
... Hey, I have a VCF format variant table produced by GATK pipeline which includes two controls and one clinical affected sample. By using selectvariant tool, it is very easy to reduce variants of the affected sample by comparing it with other two controls. However, I need to go further to reduce these ...
vcf filtering written 5.4 years ago by Tonyzeng300 • updated 4.8 years ago by Biostar ♦♦ 20
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Variant Quality Score Recalibration (Vqsr) For Non-Human Genomes
... Hey, has anyone worked with two steps of VQSR (i.e. the successive application of VariantRecalibrator and ApplyRecalibration) for the non-human genomes? You know, the human genome data have good truth and known resource datasets (HapMap
, Omni
, 1000G,
 dbSNP)
 which are already available for VQSR ...
gatk written 5.4 years ago by Tonyzeng300
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Selecting Heterozygote Calls Using Selectvariants
... Hey, I want to select heterozygotes of one sample from a variant VCF file for the homozygote selection, we used the follows, $ java -Xmx4g -jar GenomeAnalysisTK.jar -T SelectVariants -R reference.fa --mysnp.vcf -select 'vc.getGenotype("sampleID").isHomVar()' -o output.vcf & however, I use th ...
gatk written 5.4 years ago by Tonyzeng300 • updated 4.5 years ago by RamRS21k
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Comment: C: Selectvariants And Annotation Of Variants With Vcf Format
... Thank you , Sean ...
written 5.4 years ago by Tonyzeng300
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Comment: C: Per Sample Mpileup Output From Merged Bam File
... I just use samptools mpileup for single sample analaysis but not for multiple samples. Strongly suggest you to use GATK which has no such problem to recognize each of the sample for the downstream variant selections or filtering. It works very good so far with my more than 10 samples. ...
written 5.4 years ago by Tonyzeng300
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Selectvariants And Annotation Of Variants With Vcf Format
... Hey, I have a question here and want suggestions from anyone who did this before I go further. I have produced a variant VCF with many samples using GATK pipeline. Following steps will include like 1) Select two samples out of a VCF with many samplesSelect a sample 2) exclude non-variant loci 3) fi ...
gatk annotation written 5.4 years ago by Tonyzeng300 • updated 5.4 years ago by Sean Davis25k
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Is This An Error Of Ref Dbsnp?
... HI, I generated my own samples' variant or SNP calling table and plan to narrow down or filter these many of the variants using dbSNP. Here i downloaded two dbSNP with one from NCBI and another from Sanger. However, I doubt NCBI one has error when it called a nt variant change from C to T (see below ...
dbsnp ngs variant error filtering written 5.5 years ago by Tonyzeng300 • updated 5.5 years ago by Dan Gaston7.1k
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Anyone Has Used Snp & Variation Suite Of Golden Helix?
... Any one has used SNP & Variation Suite of Golden Helix? I am new for this but it seems pretty good. http://doc.goldenhelix.com/SVS/latest/index.html I have several non-human exome variant data produced by NGS pipeline. I am wondering if this tool can help me identify mutation by filtering varian ...
snp filtering written 5.5 years ago by Tonyzeng300 • updated 6 months ago by Shicheng Guo7.4k

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