User: bioinfo89

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bioinfo8940
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Posts by bioinfo89

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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 15 days ago by bioinfo8940
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Comment: C: VCF validation error:Ref allele mismatch?
... That the header I am using: ##fileformat=VCFv4.1 ##fileDate=20180926 ##dbSNP_meta_start ##TYPE:CONT ##HANDLE:xxxxxx ##NAME:xxxx ##FAX:xxxx ##TEL:xxx ##EMAIL:xxx ##LAB:xxx ##INST:xxx ##ADDR:xxx ##TYPE:PUB ##HANDLE:xxxx ##PMID:NA ##TITLE ...
written 18 days ago by bioinfo8940 • updated 17 days ago by finswimmer6.7k
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Comment: C: VCF validation error:Ref allele mismatch?
... Yes, I did check the GeneBank Accession for hg19. I am using the correct one (GCF_000001405.25). ...
written 18 days ago by bioinfo8940
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Comment: C: VCF validation error:Ref allele mismatch?
... chrMT 711 . G A . . VRT=1 this is the vcf format! ...
written 18 days ago by bioinfo8940 • updated 17 days ago by RamRS19k
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Comment: C: VCF validation error:Ref allele mismatch?
... here you go: chrM 711 711 G A ...
written 18 days ago by bioinfo8940 • updated 17 days ago by RamRS19k
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Comment: C: VCF validation error:Ref allele mismatch?
... I have used hg19 which is the same as used by dbSNP validator. ...
written 18 days ago by bioinfo8940
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VCF validation error:Ref allele mismatch?
... Hello All, I am working on submitting novel SNPs to dbSNP. When I use their online VCF validator tool I get the following error: ##ERR_REF_MISMATCH=Ref allele mismatch. Fix: need to match the reference genome on the FORWARD orientation (Expect: T, Found: G) I checked the strand infor ...
genome assembly snp written 18 days ago by bioinfo8940 • updated 18 days ago by finswimmer6.7k
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Comment: C: How to integrate GTEx data for variant annotation to understand the tissue speci
... Yes, correct. Thats exactly what I did. ...
written 4 weeks ago by bioinfo8940
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Comment: C: How to integrate GTEx data for variant annotation to understand the tissue speci
... Hi SGMS, Yes, I downloaded the metasoft file from the GTEx portal (https://storage.googleapis.com/gtex_analysis_v7/multi_tissue_eqtl_data/GTEx_Analysis_v7.metasoft.txt.gz) and corresponding rsid lookup file (https://storage.googleapis.com/gtex_analysis_v7/reference/GTEx_Analysis_2016-01-15_v7_Whole ...
written 4 weeks ago by bioinfo8940
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Comment: C: Retrieve genbank viral genomes
... Hi erwan.scoan, check out this research article ( https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3324519/ ). It has a complied list of 32102 viral genomes from GenBank, you can use it directly. Hope that helps!! ...
written 3 months ago by bioinfo8940 • updated 3 months ago by Vijay Lakhujani3.1k

Latest awards to bioinfo89

Scholar 6 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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