User: jaafari.omid

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jaafari.omid10
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Posts by jaafari.omid

<prev • 38 results • page 1 of 4 • next >
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Comment: C: vcfR for Whole Genome Data
... Thanks for the answer, So you mean I can use the vcfR package for only the vcf files which are small in size? because I have used this package for a vcf file generated for GBS data but for the WGS data I have this problem. ...
written 1 day ago by jaafari.omid10
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vcfR for Whole Genome Data
... Dears all, Actually I have a generated vcf file by samtools pipeline and before doing the filtration of SNPs, I am going to check their quality, mapping and depth using vcfR. But at the first step when I want to read the vcf file I am facing with an error. Here is the command that I used: T.vcf ...
genome R vcf snp vcfr written 1 day ago by jaafari.omid10
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Comment: C: VCF file filtration
... Thank you very much for your very helpful explanation. So I think the specificity is important to me and try to keep the final file clean. Regards, ...
written 1 day ago by jaafari.omid10
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Comment: C: VCF file filtration
... I meant my own data set, filtering my reads on vcf file based on MAF. ...
written 5 days ago by jaafari.omid10
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Comment: C: VCF file filtration
... Many many thanks for your comments. ...
written 5 days ago by jaafari.omid10
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Comment: C: VCF file filtration
... Thanks for your answer, Then can I consider the MAF by using Galaxy? ...
written 5 days ago by jaafari.omid10
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Comment: C: VCF file filtration
... So first of all I should consider those parameters. But I thought I can at least remove individuals with a specific level of missing data, also considering their minimum genotype depth and quality. For mapping I used bowtie2 with --very0sensitive option and here is the command I used for variant cal ...
written 5 days ago by jaafari.omid10
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Comment: C: VCF file filtration
... Hi, Actually I was looking to find a straightforward pipeline for filtering. Should I just do filtering for minimum genotype depth and quality? Or It is better to consider some other type of filtration?like var filtering? or removing In/Del and copy numbers? ...
written 5 days ago by jaafari.omid10
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VCF file filtration
... Dears all, I have a vcf file from whole genome data on a fish species. This vcf file has prepared with bcftools pipeline. I have read something for filtering the vcf file but I couldn't make heads or tails of them. I know there is GATK pipeline but because I used bowtie2 for mapping I am not able to ...
vcf wgs bcftools vcftools snp written 5 days ago by jaafari.omid10
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Comment: C: Calling SNPs using bcftools mpileup
... I am really grateful for your great help. Now it worked fine. Cheers, ...
written 18 days ago by jaafari.omid10

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