User: genetic

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genetic20
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United States
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2 months ago
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3 years ago
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Posts by genetic

<prev • 10 results • page 1 of 1 • next >
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GATK hg19 bundle question
... I've downloaded GATK hg19 bundle datasets. Can I use 1000G_phase1.indels.hg19.sites.vcf instead of 1000G_phase1.indels.hg19.vcf? What is difference between these 2 files? 1000G_phase1.indels.hg19.vcf 1000G_phase1.indels.hg19.sites.vcf Mills_and_1000G_gold_standard.indels.hg19.vcf Mills_and_1000 ...
gatk written 9 weeks ago by genetic20 • updated 7 weeks ago by Biostar ♦♦ 20
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Comment: C: picard installation failure
... Thank you. It works. ...
written 9 weeks ago by genetic20
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Answer: A: picard installation failure
... Hello, I've invoke it with java, but I still have an error. Could you please let me know how should I fix this? Thank you. [root@NGS:han]# java -jar picard.jar Exception in thread "main" java.lang.UnsupportedClassVersionError: picard/cmdline/PicardCommandLine : Unsupported major.minor version 52. ...
written 9 weeks ago by genetic20
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(SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
... Hello, I am working on functional annotation of my exome-chip variants. I am not sure what are the differences using annotation from (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE). ANNOVAR annotates all SNPs using refseq’s sequence information without using any algorithm. (SIFT, Polyphen, ...
genome gene snp written 22 months ago by genetic20 • updated 22 months ago by igor4.9k
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Phasing using SHAPEIT
... Hello, I need to use SHAPEIT for phasing only since I will conduct CH (compound heterozygous) analysis for recessive rare variant.. I will not perform imputation.  I am running SHAPEIT, and I see in the log file it says: Parameters :   * Seed : 1442251531   * Parallelisation: 12 threads   * Ref a ...
assembly sequence snp alignment sequencing written 2.3 years ago by genetic20
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Comment: C: PLINK results interpretation
... Yes. you guys are right. There are some samples which contain missing genotypes. Thank you! ...
written 2.4 years ago by genetic20
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PLINK results interpretation
... I found some issues in results of PLINK software. Let's say, we have 145 cases and 828 controls. I got below table using --model  and --fisher. However, I do not understand why some individuals do not included in AFF and UNAFF columns. For example, for SNP 17:74017478, 2+139=141 (I think it shou ...
software error snp written 2.4 years ago by genetic20
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Answer: A: What is the difference between fine-mapping and targeted sequencing?
... Thank you for the clarification! ...
written 2.5 years ago by genetic20
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What is the difference between fine-mapping and targeted sequencing?
... As far as I understand, targeted sequencing is for examine entire region of genes, and fine-mapping is examine certain GWAS loci. Can I say that fine-mapping is kind of targeted sequencing? Thank you, ...
next-gen snp sequencing written 2.5 years ago by genetic20
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How to convert vcf dosage file format to mldose format?
... Recently, we imputed our data using https://imputationserver.sph.umich.edu. However, since the output file format is vcf dosage data, I cannot use Mach2dat for GWAS association analysis. Does anyone know how to convert vcf dosage file format to mldose format? Thank you so much!   Dosage file fo ...
vcf imputation written 3.0 years ago by genetic20 • updated 15 months ago by lara.sucheston0

Latest awards to genetic

Popular Question 22 months ago, created a question with more than 1,000 views. For Phasing using SHAPEIT
Popular Question 22 months ago, created a question with more than 1,000 views. For What is the difference between fine-mapping and targeted sequencing?
Popular Question 22 months ago, created a question with more than 1,000 views. For (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Popular Question 22 months ago, created a question with more than 1,000 views. For How to convert vcf dosage file format to mldose format?

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