User: bioinfo89

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bioinfo8940
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Posts by bioinfo89

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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 5 weeks 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 5 weeks ago by bioinfo8940 • updated 5 weeks ago by WouterDeCoster35k
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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 5 weeks ago by bioinfo8940 • updated 5 weeks ago by WouterDeCoster35k
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Comment: C: How to merge multiple VCF files (each has multiple samples genotype) from differ
... Thanks @genomax, I will keep that in mind. ...
written 5 weeks ago by bioinfo8940
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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 5 weeks 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 ...
snp written 5 weeks ago by bioinfo8940 • updated 3 days ago by Biostar ♦♦ 20
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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 8 weeks ago by bioinfo8940
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How to convert chrM variants from NC_001807.4 version coordinates to NC_012920.1 coordinates?
... Hello All, I have few variants from chr M for which I want to convert the coordinates for these variants from previous version NC_001807.4 to the latest version NC_012920.1. Is there any way to do this? I tried using the liftover tools but I am unable to select any assembly version which is mentio ...
assembly snp written 8 weeks ago by bioinfo8940
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Comment: C: VCF validation error:Ref allele mismatch?
... I received a reply from the dbSNP people, they suggested to update the MT variants according to the latest version NC_012920 and resubmit them. ...
written 8 weeks ago by bioinfo8940
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Comment: C: VCF validation error:Ref allele mismatch?
... Thanks @finswimmer for the explanation, that was very helpful. I did ask dbsnp people for the chrM and the version for hg19 I should use. I was told to use GCF_000001405.25 and address chrM as chrMT before got this error, since I skipped the chrM version part. I will update about this once I get an ...
written 11 weeks ago by bioinfo8940

Latest awards to bioinfo89

Supporter 8 weeks ago, voted at least 25 times.
Scholar 8 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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