User: ricfoz

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ricfoz10
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Posts by ricfoz

<prev • 38 results • page 1 of 4 • next >
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Comment: C: Trouble indexing a .vcf.gz file
... it does look ok, because of the errors, i thought about sorting the vcf file, but as i look at it, all positions are in order, and i haven't change anything but the chr preffix to the chromosome number column... i think it's just about the offset of files permitted by the compiling of my bgzip tool ...
written 6 hours ago by ricfoz10
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Comment: C: Trouble indexing a .vcf.gz file
... Hello there, as expected, i have been following your suggestions, here is a description of my actual problem, since i think i know the answer, but still, as you say, it is hard with no "good" computational resources: I got online a 3.5gb.vcf.gz file which was actually already indexed, say: Ready to ...
written 6 hours ago by ricfoz10
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Comment: C: Trouble indexing a .vcf.gz file
... i wrote code with awk to add the 'chr' prefix to all the lines with information about the nucleotides, headers, say lines starting with ## at the beggining of the file weren't annotated with chr ...
written 18 hours ago by ricfoz10
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Comment: C: Trouble indexing a .vcf.gz file
... alright, i tried to run the tool with the `-p vcf` flag, and i got exactly the same error. Maybe should i find a way to sort the vcf file before compressing? .. thanks for the advice still. ...
written 23 hours ago by ricfoz10
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Comment: C: Trouble indexing a .vcf.gz file
... i tried with the -p flag, but i didn't know what input to use with the "string"option ... as i see your suggestion, the flag -p needs "vcf" as string option, i will try that syntax. Yes , i compressed it with bgzip, well, with that tool, but using GNU-parallel tool, since my compiled version of bgz ...
written 1 day ago by ricfoz10
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Comment: C: value too large for defined data type using bgzip
... Hello there, Well, i re-tried the compression, and it all seemed to go well. i have my compressed vcf.gz file, and i can view it correctly using less, so i think it's all good to go, still, i get the same error when trying to tabix index it. I already posted my trouble with that, since it is anot ...
written 1 day ago by ricfoz10
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Trouble indexing a .vcf.gz file
... Hello everyone, I am trying to index a `.vcf.gz` file in order to get a fasta consensus with `bcftools` this is the simple command i give: tabix myFile.vcf.gz and I get the next error: [E: :get_intv] failed to parse TBX_VCF, was wrong -p [type] used? The offending line was: "c" ...
vcf tabix vcf.gz compressing written 1 day ago by ricfoz10 • updated 1 day ago by Ram12k
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Comment: C: value too large for defined data type using bgzip
... That's a neat workflow suggestion, i'll try that on some complete genomes i need to work with, but i must say that the 37GB vcf file that brought the original problem in this post to me is already a one chromosome vcf file ... i think it's huge for it to be just one chr, but it actually is ... i'm r ...
written 2 days ago by ricfoz10
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Comment: C: value too large for defined data type using bgzip
... Hello, i did give the .vcf.gz extension, i'll re-run the task to see how it goes, i'll let you know the result, thank you for the interaction. The task lasted about 6 hours, so i'll be posting in a while. Cheers ...
written 2 days ago by ricfoz10
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Comment: C: value too large for defined data type using bgzip
... pfs, I know .vcf is different to .fasta format, and that fasta don't reside within .vcf files, but calling the variants inside the .vcf it's possible to generate a consensus between .vcf and the reference genome. My vcf file is a variant call file downloaded from the Max Planck Institute server. ...
written 2 days ago by ricfoz10

Latest awards to ricfoz

Scholar 17 days ago, created an answer that has been accepted. For C: getting a consense one header .fasta file from a genic region, from .bam templat

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