User: bioinfo89

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bioinfo8940
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Posts by bioinfo89

<prev • 66 results • page 1 of 7 • next >
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Comment: C: bedtools complement error
... Hi @Alex Reynolds, I was just exploring the bedpos `--complement` option instead of bedtools complement option to get coordinates which are present in `genome.bed` but not in `target.bed`, I found `--difference` is more suitable to get the `result.bed`, instead of `--complement`. Do correct me if ...
written 5 months ago by bioinfo8940 • updated 5 months ago by RamRS24k
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Comment: C: Where to get homopolymer annotation for human genome ?
... Hi @ATpoint, Thank you very much for the Rscript, I used it for extracting the homopolymers from reference genome. I wanted to know if there is a way to use the same script to limit the homopolymers finding in the coding regions only? ...
written 5 months ago by bioinfo8940
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Comment: A: Where to get homopolymer annotation for human genome ?
... Hi @ATpoint, I would really appreciate if you could share the Rscript again. I couldn't find your Rscript. Thanks! ...
written 5 months ago by bioinfo8940
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How to consider/get the g. positions for variants in introns?
... Hello All, My query is regarding the genomic positions to be considered for a variant which are present in the intron. For example: c.5278-1G>C, so the genomic position for c.5278 is 41203134. Since the above nomenclature is 5278-1 which will be 5277th position and is the last base of the intr ...
snp written 7 months ago by bioinfo8940 • updated 7 months ago by finswimmer12k
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Comment: C: Merge vcf files with multiple samples into one vcf with all variants
... Yes, I am trying my best. :) ...
written 11 months ago by bioinfo8940
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Comment: C: Merge vcf files with multiple samples into one vcf with all variants
... By non-standard vcf I mean, it is a dbSNP submission VCF format which has additional information about the study and methods etc along with the reference assembly ID, INFO and FORMAT fields. Also, the INFO and FORMAT fields I had to remove since the tabidx step was not able to parse the information. ...
written 11 months ago by bioinfo8940 • updated 11 months ago by WouterDeCoster42k
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Comment: C: Merge vcf files with multiple samples into one vcf with all variants
... Yes sure I will test the vcflib tool kit thanks for the info. I used the following commands for vcftools: /home/tools/tabix-0.2.6/bgzip Validated.vcf /home/tools/tabix-0.2.6/tabix -p vcf Validated.vcf.gz /home/tools/vcftools_0.1.13/perl/vcf-compare Validated1.vcf.gz Validated2.vcf ...
written 11 months ago by bioinfo8940 • updated 11 months ago by WouterDeCoster42k
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Comment: C: How to merge multiple VCF files (each has multiple samples genotype) from differ
... I tried it. But since the file I am using is not a standard VCF file, I am not getting the desired output. The vcf-validator throws lots of errors when I check the files I am using. ...
written 11 months ago by bioinfo8940
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Merge vcf files with multiple samples into one vcf with all variants
... Hi All, I am working on 1000g data. So I have 25 tab-delimited text files corresponding to each population. Each file has jointly genotyped data, so it contains genotypes from all the samples (~60-120) per population in the VCF. Format of the File: #CHROM POS ID REF ALT QUAL FILTER INFO FORMA ...
vcf snp written 11 months ago by bioinfo8940 • updated 8 months ago by zx87548.4k
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Comment: C: How to convert chrM variants from NC_001807.4 version coordinates to NC_012920.1
... Yes that's true but the hg19 reference (UCSC version) uses NC_001807 version for chrM mentioned here : http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/. It has not been updated to the NC_012920.1 for hg19. This is the reason why I want to convert my variants to the latest version but I am no ...
written 12 months ago by bioinfo8940

Latest awards to bioinfo89

Popular Question 7 months ago, created a question with more than 1,000 views. For Merge vcf files with multiple samples into one vcf with all variants
Popular Question 7 months ago, created a question with more than 1,000 views. For Primer3 error:./primer3_core: Input line with no '=':
Popular Question 9 months ago, created a question with more than 1,000 views. For Primer3 error:./primer3_core: Input line with no '=':
Supporter 12 months ago, voted at least 25 times.
Scholar 18 months ago, created an answer that has been accepted. For A: How to extract unique paired end reads from a merged BAM file?

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