User: prasundutta87

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prasundutta87360
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Posts by prasundutta87

<prev • 153 results • page 1 of 16 • next >
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soft-clipping during alignment and variant calling query
... It is known that BWA-MEM soft-clips bases to achieve a higher alignment rate. If a variant caller is used after that, say, GATK Haplotyecaller, is it necessary to keep the parameter --dont-use-soft-clipped-bases to TRUE? Or should we keep it in default (false) as it may affect the realignment step d ...
variant calling bwa-mem alignment gatk written 27 days ago by prasundutta87360 • updated 3 days ago by Biostar ♦♦ 20
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Answer: A: allele specific expression (ASE) reference ratio plot query
... Just to update on this, the first two weird plots arose due to sample switching in the lab.. ...
written 4 months ago by prasundutta87360
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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 6 months ago by prasundutta87360 • updated 5 months 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 8 months ago by prasundutta87360 • updated 8 months ago by RamRS24k
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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 8 months ago by prasundutta87360 • updated 3 months ago by Biostar ♦♦ 20
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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 8 months ago by prasundutta87360
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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 8 months ago by prasundutta87360
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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 9 months ago by prasundutta87360
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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 9 months ago by prasundutta87360
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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 9 months ago by prasundutta87360

Latest awards to prasundutta87

Popular Question 22 days ago, created a question with more than 1,000 views. For fastqc adapter content
Popular Question 6 weeks ago, created a question with more than 1,000 views. For fastqc adapter content
Popular Question 8 weeks ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Student 11 weeks ago, asked a question with at least 3 up-votes. For allele specific expression (ASE) reference ratio plot query
Popular Question 3 months ago, created a question with more than 1,000 views. For HISAT2 (v2.0.0-beta) MAPQ query for allele specific expression analysis
Popular Question 8 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Scholar 10 months ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
Popular Question 11 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Scholar 11 months ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
Student 13 months ago, asked a question with at least 3 up-votes. For allele specific expression (ASE) reference ratio plot query
Popular Question 13 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Popular Question 14 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Popular Question 15 months ago, created a question with more than 1,000 views. For HISAT2 MAPQ scoring scheme
Centurion 16 months ago, created 100 posts.
Supporter 18 months ago, voted at least 25 times.
Scholar 2.3 years ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: SNPEFF for de novo transcriptome annotation

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