User: r00628112

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r0062811210
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Posts by r00628112

<prev • 11 results • page 1 of 2 • next >
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Comment: C: The genotype imputation in Beagle always stop on specific step and can not finis
... Ok. Thank you. There are no error message, but an WARNING message showed during processing. (in this photo https://drive.google.com/open?id=1osAetLl0rSG9FlfvnAwlEp3dZm-ZFVc6) And the stop site information are as below: (1) The stop site in the original VCF file: https://drive.google.com/open?id=1bH ...
written 9 days ago by r0062811210
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Comment: C: The genotype imputation in Beagle always stop on specific step and can not finis
... Sure. Thank you so much. (1) The stop site in the original VCF file: https://drive.google.com/open?id=1bHWom4I_ztD5wTMNti9bHvFwRa6eaz8Z (2)The stop site in the beagle imputation file https://drive.google.com/open?id=1RFnAY3ljjykRmibkl7cmz5z4RL-cvAXK ...
written 9 days ago by r0062811210
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Comment: C: The genotype imputation in Beagle always stop on specific step and can not finis
... Hi~ Thanks to your reply. I checked the vcf file, and there are no any NaN characters. Then, I followed the solution from the link (add -Xss5m), but it is no work. Thank you very much :D ...
written 11 days ago by r0062811210
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The genotype imputation in Beagle always stop on specific step and can not finish the imputation file
... Hello~ About the genotype imputation in Beagle, I run the vcf file, but the program always stopped in this step as the attached link.(https://drive.google.com/open?id=1osAetLl0rSG9FlfvnAwlEp3dZm-ZFVc6) I used this command: java -jar beagle.25Nov19.28d.jar gt=200212-NiNK_newPmgenomeDP5Q10maf ...
imputation genotype beagle written 11 days ago by r0062811210 • updated 9 days ago by Kevin Blighe54k
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About beagle imputation
... Hi~ everyone I would like to impute the vcf file for further analysis. I used the code as below: java -jar beagle.25Nov19.28d.jar gt=191122-NKSC_newPmgenome.vcf out=Impt-191122-NKSC_newPmgenome.vcf impute=TRUE The information showed: Command line: java -Xmx27305m -jar beagle.25Nov19.28d ...
imputation beagle written 12 days ago by r0062811210 • updated 12 days ago by ATpoint29k
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How to convert the VCF file into the haplotype format?
... Hello~ everyone As the title mentioned, does anyone know how to convert the VCF file into this kind of haplotype format as the attached figure(https://www.dropbox.com/s/8o2yt6gbikocjo2/200123-haplotype.png?dl=0) [haplotype figure][1] ![figure][2] [1]: https://www.dropbox.com/s/8o2yt6gbikocjo2/ ...
vcf haplotype written 4 weeks ago by r0062811210 • updated 4 weeks ago by Kevin Blighe54k
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About the method for removing the SNP markers with more than 10% of missing data?
... Hi~ everyone. For the QTL analysis, I conducted the GBS getting SNP markers for the establishment of the genetic map. However, there are some SNP markers with too much missing data, I would like to discard these SNPs. Is there any tool that can discard the SNP markers with more than 10% of missin ...
vcf qtl snp written 6 weeks ago by r0062811210
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How to establish a new annotation library in snpEff
... Hello~ Good afternoon I would like to analyze the variant sequences in Prunus mume. How to eatablish the annotation library of Prunus mume in snpEff? Thank you ...
snpeff written 9 weeks ago by r0062811210
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How to calculate the SNP/Indel number between cultivars by using combined VCF file?
... I would like to follow this paper to do the analysis of Genome-wide DNA polymorphisms by using four cultivars re-sequencing data. I would like to make this kind of table and picture in this paper [Table 2 Frequency of SNPs and InDels detected in PSRR-1, Bengal, and Nona Bokra.][1], [Figure 1 Genome- ...
genome vcf indel snp written 11 weeks ago by r0062811210 • updated 11 weeks ago by David Minkley10
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Comment: C: How to filter SNP and Indel under these criteria?
... Thanks to your suggestion. Because of limited data, I would like follow this paper to do the analysis of Genome-wide DNA polymorphisms by using four cultivars re-sequencing data. I would like make this kind of table and picture in this paper, thus I'm curious about how to comparing the SNP or Inde ...
written 3 months ago by r0062811210

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