User: prasundutta87

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prasundutta87330
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Posts by prasundutta87

<prev • 151 results • page 1 of 16 • next >
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finding out SNPs from SNVs and breed specific SNPs
... Hi, I am working with a multisample VCF file for a non-model organism that contains only biallelic single nucleotide variants (SNVs). The samples belong to different breeds of the organism as well. I wish to find SNPs (single nucleotide polymorphisms), which is a population-based term (the SNV shoul ...
snv snp written 9 weeks ago by prasundutta87330 • updated 5 weeks ago by Biostar ♦♦ 20
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Answer: C: I can not run bcftools stats (help)
... '-s' stands for **list of samples for sample stats** The command expects sample names and not the VCF file as you have written. The correct command should be bcftools stats -F "My_reference_genome.fasta" -s - "My_vcf.gz_file.vcf.gz" > "/T1_.vcf.stats" This would of course give you stats ...
written 3 months ago by prasundutta87330 • updated 3 months ago by RamRS22k
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candidate region selection in an XP-EHH analysis
... Hi, In an XP-EHH analysis, whenever a high scoring peak is observed, it's a practice to capture the candidate region around the highest scoring SNP and check which genes are present. How many base pairs upstream and downstream should be checked? Different papers follow different values. What is the ...
snp xp-ehh written 3 months ago by prasundutta87330
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Comment: C: outliers in XP-EHH
... Thanks for this..the thing is somehow there is no one appropriate way to detect outliers for this kind of analysis..many papers have used different techniques..could not find a consensus. ...
written 3 months ago by prasundutta87330
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outliers in XP-EHH
... Whenever you perform an XP-EHH analysis involving populations, you tend to perform many pairwise XP-EHH calculations. During those scenarios, what is the best way to detect outliers? Currently, for all pairwise comparison, the XP-EHH scores were calculated per chromosome. the scores were converted ...
population genetics outliers xp-ehh written 3 months ago by prasundutta87330
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Comment: C: Difference between Private SNPs and Singleton SNPs
... I used the GATK germline variant calling pipeline to generate my VCF file. Is any more information needed? ...
written 4 months ago by prasundutta87330
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Comment: C: Difference between Private SNPs and Singleton SNPs
... Thanks Giovanni. Do you know how are Private variants found or how they are assigned to a population in a VCF file? I know that Snpsift has a tool called 'private' that does that. But do you know what methodology does it follow to achieve that? ...
written 4 months ago by prasundutta87330
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Difference between Private SNPs and Singleton SNPs
... Hi, I was wondering if anyone can let me know the difference between 'Private' SNPs and 'Singleton' SNPs in a VCF file. For example, if I have a multisample VCF file of 20 samples, containing samples from different populations/families..say family A and family B each consisting of 10 individuals ea ...
variant calling gatk snps snp population genetics written 4 months ago by prasundutta87330
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Correct way to report variant statistics from bcftools stats report
... Hi, I am making a table of family-wise variants statistics. I have a multisample VCF file of biallelic SNPs on which I ran BCFtools v1.6 using the following command. bcftools stats -s - This gives me the following output (edited for brevity): sample nRefHom nNonRefHom nHets family_ ...
bcftools snp variants statistics written 4 months ago by prasundutta87330
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Comment: C: PCAtools: everything Principal Components Analysis
... Understandable..Thanks a lot Kevin.. ...
written 4 months ago by prasundutta87330

Latest awards to prasundutta87

Popular Question 4 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Scholar 5 months ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
Popular Question 6 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Scholar 7 months ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
Student 8 months ago, asked a question with at least 3 up-votes. For allele specific expression (ASE) reference ratio plot query
Popular Question 9 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Popular Question 9 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Popular Question 10 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Centurion 11 months ago, created 100 posts.
Supporter 14 months ago, voted at least 25 times.
Scholar 22 months ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: SNPEFF for de novo transcriptome annotation

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