vcf to MAF to fasta

Question: vcf to MAF to fasta

4.8 years ago by

natasha.sernova • 3.4k

natasha.sernova • 3.4k wrote:

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

galaxy vcf • 2.9k views

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modified 4.8 years ago by Biostar ♦♦ 20 • written 4.8 years ago by natasha.sernova • 3.4k

4.8 years ago by

Pierre Lindenbaum ♦ 120k

France/Nantes/Institut du Thorax - INSERM UMR1087

Pierre Lindenbaum ♦ 120k wrote:

"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

ADD COMMENT • link written 4.8 years ago by Pierre Lindenbaum ♦ 120k

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

ADD REPLY • link written 4.8 years ago by natasha.sernova • 3.4k

is -L required ?

ADD REPLY • link written 4.8 years ago by Pierre Lindenbaum ♦ 120k

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

ADD REPLY • link written 4.8 years ago by natasha.sernova • 3.4k

"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

ADD REPLY • link written 4.8 years ago by Pierre Lindenbaum ♦ 120k

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!

ADD REPLY • link written 4.8 years ago by natasha.sernova • 3.4k

I guess I missed the goal of OPs question, I just was not sure what they wanted in the fasta file. I presumed that they didn't have a preexisting fasta file with their reference sequences.

ADD REPLY • link written 4.8 years ago by pld ♦ 4.8k

4.8 years ago by

pld ♦ 4.8k

United States

pld ♦ 4.8k wrote:

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.

ADD COMMENT • link written 4.8 years ago by pld ♦ 4.8k

The Multiple Alignment Format (MAF) has been used by UCSC/EnsEMBL etc for ten years or so. It is one of the most widely used multi-alignment formats. The first spec for the Mutation Annotation Format was only released two years ago.

ADD REPLY • link modified 4.8 years ago • written 4.8 years ago by lh3 ♦ 31k

https://wiki.nci.nih.gov/dosearchsite.action?queryString=Multiple+alignment+format
So my question doesn't make sence at all. OK, thank you.

ADD REPLY • link written 4.8 years ago by natasha.sernova • 3.4k

That link just leads me to Mutation Annotation Format.

ADD REPLY • link written 4.8 years ago by pld ♦ 4.8k

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