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Search: Posts Made By: XeroxHero69
Forum: Bioinformatics 05-31-2019, 09:57 AM
Replies: 4
Views: 472
Posted By XeroxHero69
Thank you so much, this seems the route I need to...

Thank you so much, this seems the route I need to take!
Forum: Bioinformatics 05-28-2019, 10:35 AM
Replies: 4
Views: 472
Posted By XeroxHero69
How to regenerate an index file for a gzipped vcf file?

I have a large vcf file with genomic data (330 GB) and an index file that accompanies it. I ran the command:

bcftools view -f PASS --threads 8 -r chr9:55252802-55252810 -o output.vcf.gz -O z...
Forum: Bioinformatics 05-07-2019, 10:41 AM
Replies: 1
Views: 525
Posted By XeroxHero69
bcftools output type not recognized

I am trying to find a single SNP on a bunch of dog genomes in a compressed vcf file (vcf.gz) and I have been using bcftools to do so. I posted ...
Forum: Bioinformatics 05-06-2019, 10:44 AM
Replies: 12
Views: 955
Posted By XeroxHero69
So do I need to create a new file for the output...

So do I need to create a new file for the output prior to running this command? how would the command look if I use -v without overwriting my file again. Sorry if these are simple questions. Thanks!
Forum: Bioinformatics 05-06-2019, 08:58 AM
Replies: 12
Views: 955
Posted By XeroxHero69
So to make sure I do it right this time, what do...

So to make sure I do it right this time, what do I do to make the .vcf.bgz file?
Forum: Bioinformatics 05-01-2019, 10:22 AM
Replies: 12
Views: 955
Posted By XeroxHero69
Thanks so much. I tried this command: ...

Thanks so much. I tried this command:

bcftools view -f PASS --threads 8 -r chr9:55252802-55252802 -o 722g.990.SNP.INDEL.chrAll.vcf.gz -O z 722g.990.SNP.INDEL.chrAll.vcf.gz

and it returned: ...
Forum: Bioinformatics 05-01-2019, 09:23 AM
Replies: 1
Views: 407
Posted By XeroxHero69
bcftools view to find a base at a certain position for a set of samples

I have a humongous vcf.gz file with a bunch of whole genome sequences of dogs. I want to find a base at a specific position for a select number of those samples. I think that I should use -t/-T to...
Forum: Bioinformatics 05-01-2019, 09:16 AM
Replies: 12
Views: 955
Posted By XeroxHero69
Thanks for your reply. Could you give me an...

Thanks for your reply. Could you give me an example of the format of what a command that would use bcftools view to find a base at a position would look like?
Forum: Bioinformatics 04-30-2019, 11:04 AM
Replies: 12
Views: 955
Posted By XeroxHero69
So I have bcftools installed. I want to check for...

So I have bcftools installed. I want to check for a single-replacement mutation on a specific gene in each of the genomes in the file. Do you know of a way to do this using bcftools? I am new to...
Forum: Bioinformatics 04-30-2019, 09:09 AM
Replies: 12
Views: 955
Posted By XeroxHero69
Thanks so much, I'll try this out :)

Thanks so much, I'll try this out :)
Forum: Bioinformatics 04-29-2019, 11:34 AM
Replies: 12
Views: 955
Posted By XeroxHero69
Accessing Genomic data in a large vcf.gz file

Hello all, I am very new to bioinformatics; I'm a high school intern. I have a .vcf.gz file that is 332 GB. It contains the whole genomes of around 800 dogs and all I need to do is check for a...
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