User: Sudhir Jadhao

gravatar for Sudhir Jadhao
Reputation:
60
Status:
Trusted
Location:
India
Last seen:
2 days, 10 hours ago
Joined:
4 years, 2 months ago
Email:
s***************@gmail.com

Posts by Sudhir Jadhao

<prev • 57 results • page 1 of 6 • next >
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SNP calling in Identical exons of two different genes
... Hello Everyone, I am calling germline mutation using BWA and GATK pipeline. RHD and RHCE gene share 97% homology. The exon2 and exon8 of these genes are identical. So there is a high chance that the reads from these regions may map to each other and call false negative SNPs How can I differentia ...
genome homolog alignment snp identical exon written 8 days ago by Sudhir Jadhao60
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Comment: C: How to calculate Minor Allele Frequency (MAF) for your own population data
... Thank you, Kevin, this answers my main question.!! ...
written 5 months ago by Sudhir Jadhao60
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Comment: C: How to calculate Minor Allele Frequency (MAF) for your own population data
... The calculation you explained is with respect to all samples? Means the "If (AF < 0.5) then MAF = AF" 0.5 MAF of that particular allele is with respect to all sample present in VCF? ...
written 5 months ago by Sudhir Jadhao60
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Comment: C: How to calculate Minor Allele Frequency (MAF) for your own population data
... Can you explain it in little details with respect to MAF? ...
written 5 months ago by Sudhir Jadhao60
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Comment: C: How to calculate Minor Allele Frequency (MAF) for your own population data
... Thank again Kevin, What is the source of your VCF? => The file created using below command( merging of multiple vcf): java -jar ~/Tools/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef/GenomeAnalysisTK.jar -T CombineVariants -R ~/Database2/HG19_UCSC/hg19/Sequence/Chromosomes/GATK_UCSC_HG19.fasta --varia ...
written 5 months ago by Sudhir Jadhao60 • updated 5 months ago by Kevin Blighe37k
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(Closed) bcftools: plugins/fill-tags.c:432: process: Assertion `rec->n_allele < 8*sizeof(int)' failed. #882
... I am running below command: bcftools +fill-tags Cases.vcf >Cases_MAF_bcftools.vcf output: bcftools: plugins/fill-tags.c:432: process: Assertion `rec->n_allele < 8*sizeof(int)' failed. Aborted (core dumped) There are some threads available regarding the same issue but I am not able to unde ...
bcftools written 5 months ago by Sudhir Jadhao60
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Comment: C: How to calculate Minor Allele Frequency (MAF) for your own population data
... Thank you, Kevin!!! I think it will help I trying to run bcftools but I got below error: bcftools: plugins/fill-tags.c:432: process: Assertion `rec->n_allele < 8*sizeof(int)' failed. Aborted (core dumped) Trying to solve the error. Once the error is solved I will get back to you!! ...
written 5 months ago by Sudhir Jadhao60
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Comment: C: How to calculate Minor Allele Frequency (MAF) for your own population data
... Thank you, Nitin!! Will try to calculate manually using the mentioned formula in the link ...
written 5 months ago by Sudhir Jadhao60
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How to calculate Minor Allele Frequency (MAF) for your own population data
... Dear All, I have a VCF file containing 60 samples. I want to calculate MAF for each variant with respect to 60 samples present in a VCF file. Can anyone please tell me how to calculate MAF for you own population data? Thank you In advance for your help ...
vcf maf written 5 months ago by Sudhir Jadhao60 • updated 5 months ago by Kevin Blighe37k
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Comment: C: NCBI Genome Remapping Service- clinical remap
... Thank you @fin and @Emily_Ensembl, I have tried Ensembl's VEP before also but it is not converting all my input RefSeq to hg19, for only a few inputs it's working. In will contact NCBI support, will see their reply ...
written 7 months ago by Sudhir Jadhao60

Latest awards to Sudhir Jadhao

Popular Question 4 months ago, created a question with more than 1,000 views. For Chipseq data with Mock, Input And IP
Popular Question 9 months ago, created a question with more than 1,000 views. For Chipseq data with Mock, Input And IP
Popular Question 17 months ago, created a question with more than 1,000 views. For Plasmid Genome Assembly
Popular Question 17 months ago, created a question with more than 1,000 views. For Chipseq data with Mock, Input And IP
Popular Question 23 months ago, created a question with more than 1,000 views. For Plasmid Genome Assembly
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Plasmid Genome Assembly
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Plasmid Genome Assembly
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Metaseq: Average ChIP-seq signal over promoters error
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Metaseq: Average ChIP-seq signal over promoters error

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