User: kirannbishwa01

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Posts by kirannbishwa01

<prev • 207 results • page 1 of 21 • next >
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Answer: A: Is this GT a mistake?
... Standard practice differs depending upon what is the purpose of your data analyses: - Are you doing hard filtering? - What is the threshold while doing hardfiltering? - Are you will to assign the variants as reference if the confidence for alternate is low. Vs. Are you willing to leave the low conf ...
written 7 days ago by kirannbishwa01620
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Comment: C: Is this GT a mistake?
... Read the `bcftools` documentation, and the corresponding output for the given `sub commands`. All you have to do is read into the mechanistic details of what the tools does for the given subcommand. ...
written 8 days ago by kirannbishwa01620
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Answer: A: Is this GT a mistake?
... Well, whatever pipeline you used must be filtering the genotypes. If you look at the `AD` tag of `FORMAT` field you have **24 reads supporting allele 0 - reference allele** and **23 reads supporting allele number 2 - the second alternate allele**. So, the pipeline you used must be retesting this alt ...
written 8 days ago by kirannbishwa01620
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Explanation of the markov chain in the given plot.
... I am trying to run a markov process. I came across this webpage https://martin-thoma.com/python-markov-chain-packages/, which details a simple case of markov process in R and python. While all the details are clear to me including 1) genotype of the children from given diploid parental cross 2) pres ...
R markov chain markov process python plot written 8 days ago by kirannbishwa01620
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Comment: C: How to update the INFO field of VCF after merging, subsetting?
... Ram compare the given two VCF output at same site: vcf-merge ms01e_phased.vcf.gz ms02g_phased.vcf.gz ms03g_phased.vcf.gz ms04h_phased.vcf.gz > F1.phased_variants.Final02.vcf #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ms01e ms02g ms03g ms04h 2 15881550 . C T 7920.03 PASS AC=1;AF=0 ...
written 16 days ago by kirannbishwa01620 • updated 16 days ago by Ram13k
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How to update the INFO field of VCF after merging, subsetting?
... I am running into problem which has been asked in this forum but no right solution has be provided so far. I have to regularly subset and merge several samples vcf during my data processing. But, I realize that a important information like `AF - allele frequency`, `AC - allele count` etc. aren't ge ...
vcf genome merge vcftools info written 17 days ago by kirannbishwa01620 • updated 14 days ago by jd10.work0
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Udpate the FILTER field in VCF to PASS if the variants is represented as true in another set of VCF?
... I have a VCF files called from several samples (Say Vcf01), and also have a VCF files with sites that are true variants (Say Vcf02). So, what I want to do is update the `FILTER` field for the sites in Vcf01 to `PASS` if the variants is represented in Vcf02. I have checked several VCF tools and als ...
vcf snp pass written 4 weeks ago by kirannbishwa01620 • updated 4 weeks ago by Pierre Lindenbaum103k
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Comment: C: looking for alignment in IGV
... I am little confused over the question but would like to help in someway. - You need to specify if the reads that were aligned were single end vs. paired end and the size. - If you are using illumina paired ends (which are the longest possible in illumina) how come even a paired end read cover 200 ...
written 8 weeks ago by kirannbishwa01620
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Comment: C: How to name the genome in karyoploteR ?
... It worked for lyrata the way you explained. Now, again it doesn't work for thaliana. > karyoploteR::plotKaryotype(genome = Athaliana) Error in is(genome, "GRanges") : object 'thaliana' not found I think the problem is with the naming, and I cannot find the right way. Why is there diffe ...
written 9 weeks ago by kirannbishwa01620
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Comment: C: Some clarification on enrichment analyses and pathway analyses?
... Hi Kevin, Can you tell me what tool was used to generate these plots and link to this plot, so I can check some description. Thanks, ...
written 9 weeks ago by kirannbishwa01620

Latest awards to kirannbishwa01

Appreciated 7 weeks ago, created a post with more than 5 votes. For A: How to plot coverage and depth statistics of a bam file
Popular Question 7 weeks ago, created a question with more than 1,000 views. For How to add custom fields to the VCF files?
Popular Question 9 weeks ago, created a question with more than 1,000 views. For How to add custom fields to the VCF files?
Popular Question 11 weeks ago, created a question with more than 1,000 views. For How to add custom fields to the VCF files?
Popular Question 3 months ago, created a question with more than 1,000 views. For error while using picard 2.1.0
Popular Question 4 months ago, created a question with more than 1,000 views. For How to select aligned reads below certain mapping Quality (from BWA)?
Popular Question 4 months ago, created a question with more than 1,000 views. For How to select aligned reads below certain mapping Quality (from BWA)?
Popular Question 5 months ago, created a question with more than 1,000 views. For How to remove kmer profiles?
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Scholar 7 months ago, created an answer that has been accepted. For A: How to select aligned reads below certain mapping Quality (from BWA)?
Popular Question 8 months ago, created a question with more than 1,000 views. For How to remove kmer profiles?
Popular Question 9 months ago, created a question with more than 1,000 views. For Changing @RG header information in *.bam files using picard
Scholar 9 months ago, created an answer that has been accepted. For A: How to select aligned reads below certain mapping Quality (from BWA)?
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: How to plot coverage and depth statistics of a bam file
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Bedtools Genomecoveragebed Usage : How To Create A Genome File?
Appreciated 11 months ago, created a post with more than 5 votes. For A: How to plot coverage and depth statistics of a bam file
Scholar 12 months ago, created an answer that has been accepted. For A: How to select aligned reads below certain mapping Quality (from BWA)?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How to plot coverage and depth statistics of a bam file
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: How to plot coverage and depth statistics of a bam file
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Scholar 16 months ago, created an answer that has been accepted. For A: How to select aligned reads below certain mapping Quality (from BWA)?

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