User: nagarsaggi

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nagarsaggi10
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Posts by nagarsaggi

<prev • 11 results • page 1 of 2 • next >
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how to estimate heterozygosity by sample from a multi-sample vcf file
... Hi All, I want to estimate heterozygosity by samples from a multisample vcf file. I mapped whole-genome short reads data of many samples to a reference genome and did joint variants calling using freebayes which outputted a multisample vcf file. I would like to calculate % heterozygosity for each sa ...
snp written 6 weeks ago by nagarsaggi10 • updated 6 weeks ago by trausch1.4k
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How could I get population or individual specific genotypes from multi sample VCF file
... I build a neighbour-joining tree from a multi-sample (genotype) vcf file and could see the population structure in the samples. I was wondering if I could extract population-specific variant/genotype information from vcf file (present in one population but absent in other). ...
snp written 4 months ago by nagarsaggi10
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Comment: C: sorting a multi-sample (genotype) vcf file
... It worked perfectly! Thanks ...
written 4 months ago by nagarsaggi10
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sorting a multi-sample (genotype) vcf file
... I have a freebayes genotyped multisample vcf file. I want to sort the names of the samples in alphabetical order to make my life a bit easy with post variant calling analysis. I have tried Picared SortVcf which work fine which works fine on a small file but failed on a large file (~4 Gb). If you sug ...
snp written 4 months ago by nagarsaggi10
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Comparing the size of assemblies, contiguity and busco stats of multiple isolates genome
... I have the spades assembly of 109 samples of a plant pathogenic fungi. I have done BUSCO analysis for all the isolates. I want to compare the size of the assembly and contiguity with the size of the input data. How do I calculate and extract the assembly stats of each isolate in a tabular form? I a ...
assembly written 13 months ago by nagarsaggi10 • updated 13 months ago by jean.elbers1.3k
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Getting consensus fasta sequence for a chromosome from a bam file
... I have a bam file per sample which I have generated by mapping Illumina short reads on ~1100 single copy orthologues genes (busco). I want to extract consense sequence from bam file for a given single copy orthologue, in another way for a given chromosome. The aim is to generate a multiple sequence ...
alignment written 18 months ago by nagarsaggi10 • updated 18 months ago by finswimmer13k
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Comment: C: how to count variants par sample per chromosome in a vcf file?
... Yes, I tried this but still get same number of variant per site for all individual samples. ...
written 19 months ago by nagarsaggi10
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Comment: C: Plotting SNP density along a chromosome from VCF files
... Hi Sacha, I also want to do something similar but I for each sample from a multisample vcf file. I tried extracting a single sample from the multi-vcf file and then followed your command but the number of variants counts for different samples remain the same (probably these are the sites where a var ...
written 19 months ago by nagarsaggi10
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Comment: C: how to count variants by chromosome in a vcf file?
... Thank JC for the prompt reply, but with this commend, I get same number of the variants on each chromosome across the samples. The commend counts all the chromosome sites where a variants is called across the samples which would be same for all the samples. What I want is the number of the variants ...
written 19 months ago by nagarsaggi10
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Comment: C: normalization of Single Nucleotide Variation number based on chromosome length
... I am trying to do the same! If you do it, could yow let me know. Thanks ...
written 19 months ago by nagarsaggi10

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Popular Question 11 months ago, created a question with more than 1,000 views. For how to count variants par sample per chromosome in a vcf file?

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