User: Nupur G

gravatar for Nupur G
Nupur G30
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6 years, 9 months ago
Joined:
6 years, 10 months ago
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Posts by Nupur G

<prev • 5 results • page 1 of 1 • next >
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Answer: A: Vcf-Consensus To Generate Consensus File
... Yes I am...I looked in the code, and it seems that it was a QC check that it was failing it. So I commented it. But not sure if that is a good thing. ...
written 6.8 years ago by Nupur G30
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Vcf-Consensus To Generate Consensus File
... I have a VCF file and a reference fasta file, and am trying to create a consensus sequence using vcf-consensus. First I create a tabix file, and then I run cat NC_002516.2.fa | vcf-consensus 1_e5_d30.vcf.gz > out.fa and I get an error The fasta sequence does not match the REF at NC_002516.2:8 ...
vcf consensus next-gen written 6.8 years ago by Nupur G30 • updated 3.4 years ago by Biostar ♦♦ 20
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Comment: C: Vcf Locations In Consensus Sequence
... Thanks for the input. Yes, I think I will write my own script. I just thought there might be a way to do this by an existing tool, as it is possibly a common enough task. ...
written 6.8 years ago by Nupur G30
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Comment: C: Vcf Locations In Consensus Sequence
... You're right - but this is true only for SNPs. Indels will cause shifting. ...
written 6.8 years ago by Nupur G30
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Vcf Locations In Consensus Sequence
... I have a VCF file created by running GATK on read files against a reference genome. The variants in the VCF file have 'locations', these are the locations on the reference genome. Sample lines include NC_002516.2 92915 . T A 1941.76 PASS AC=2;AF... GT:AD:DP:GQ:PL 1/1:0,80 ...
consensus vcf next-gen variant written 6.8 years ago by Nupur G30 • updated 5.5 years ago by Jorge Amigo11k

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