Dear all,
A strange idea has came to my mind recently.
There is no direct way to convert vcf into fasta. But
I've read that through Galaxy I can convert vcf to maf (multiple align),
and then it may be possible to convert maf to fasta.
How much information from the original vcf-file will I loose using this way,
and is it possible to avoid the loss?
THANK YOU!
Natasha
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natasha.sernova
"There is no direct way to convert vcf into fasta" : there is. The GATK provides a tool named FastaAlternateReferenceMaker http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_fasta_FastaAlternateReferenceMaker.html
Yes, that's true. I've even used it once.
But this option killed me.
-L input.intervals \ I still haven't known (if I have a particular vcf-file number 1), how and where to find the corresponding interval coordinates.
You definitely know. PLEASE, help me!
Thank you very much indeed!
Natasha
is -L required ?
Dear Pierre,
this is optional parameter. But when I omit it, I have just the full fasta-fail for corresponding chromosome, nothing else. I thought that GATK will allow me to cut a fragment corresponding.to vcf-file. But I have to give it "one or more genomic intervals over which to operate". It seems much more complicated. How to find these genomic intervals?
I have vcf-files, refs and chromosome sequences. I made fai-files, dict-files, but it still doesn't give me any hints to the fasta alignment. What else should be done?
Many thanks for your help!
Natasha
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natasha.sernova
"one or more genomic intervals over which to operate": I don't understand your problem. You can provide a BED file or even a VCF file: http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_CommandLineGATK.html#--intervals
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Pierre Lindenbaum
Great. And this will work??? " In order to perform the analysis
at specific positions based on the records present in the file
(e.g. -L file.vcf)" - this is exactly what I need. I will try, that's a miracle.
I was very poor in reading the manual... THANK YOU, Pierre!
MAF is Mutation Annotation Format, not a multiple alignment:https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+%28MAF%29+Specification+-+v2.4
Fasta is really a flat sequence data format, you might be able to store the variants found in a sequence in the fasta header, but I'm not sure what you're asking for makes sense.
https://wiki.nci.nih.gov/dosearchsite.action?queryString=Multiple+alignment+format
So my question doesn't make sense at all. OK, thank you.
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natasha.sernova
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