How do I get a GFF file

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4.8 years ago

apl00028 ▴ 90

I need GFF file from my vcf file but I do not how to get them or for what? What program should I use?

Thanks in advantage.

snp • 3.6k views

ADD COMMENT • link 4.8 years ago by apl00028 ▴ 90

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I need GFF file from my vcf file

As posed this question does not make a lot of sense. VCF files describe polymorphisms compared to a reference, where as GFF files are used for describing gene models/annotations. They are not directly inter-convertible.

What exactly are you trying to do?

ADD REPLY • link 4.8 years ago by GenoMax 141k

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You are right, I am sorry. I trying to analyze my polimorfism data using this commands in R:

            chrom <- create.chromR(name='Supercontig', vcf=vcf, seq=dna, ann=gff)

For do that I need the vcf file, the reference sequence and the gff file of my vcf file, but I do not how to get that.

I got that code from here: https://cran.r-project.org/web/packages/vcfR/vignettes/intro_to_vcfR.html

ADD REPLY • link 4.8 years ago by apl00028 ▴ 90

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the gff file of my vcf file

You actually need a GFF file for the reference genome you used to create that VCF file. Generally recommended that you get GFF from the same source where you got the reference from, so there are no discrepancies with chromosomal identifiers etc.

ADD REPLY • link 4.8 years ago by GenoMax 141k

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which program should do I use for that?

ADD REPLY • link 4.8 years ago by apl00028 ▴ 90

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What genome are you working with and where did you get the reference sequence from?

ADD REPLY • link 4.8 years ago by GenoMax 141k

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My reference sequence I got for an assembly of my data

ADD REPLY • link 4.8 years ago by apl00028 ▴ 90

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You probably have some additional work to do then. Get the RefSeq assembly for this virus from NCBI. You will also find a GFF file in that same directory.

Compare your assembly with the reference and depending on changes you see you could modify the GFF file available for RefSeq genome and use that.

ADD REPLY • link 4.8 years ago by GenoMax 141k

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You need to tell us more about your data first. We need far more information.

What organism? Where did you get the VCF? How was the VCF derived? From what sequence?

ADD REPLY • link 4.8 years ago by Joe 21k

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The organism is Cucumber Mosaic Virus RNA3, I got this vcf file from bam file using these functions:

samtools mpileup -g -f scaffold_nofilt_PV014_OD_DB.fa scaffold_nofilt_OD_PV067.bam >scaffold_nofilt_OD_PV067_q10_variant.bcf

bcftools view -v -c -g scaffold_nofilt_OD_PV067_q10_variant.bcf > scaffold_nofilt_OD_PV067_q10_variant.vcf

ADD REPLY • link updated 4.8 years ago by Joe 21k • written 4.8 years ago by apl00028 ▴ 90

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So this is a genome you de novo assembled?

ADD REPLY • link 4.8 years ago by Joe 21k

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Yes, using IDBA_UD program

ADD REPLY • link 4.8 years ago by adrian.pelaezl • 0

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Hi, are you the same person as the user apl0028?

ADD REPLY • link 4.8 years ago by Ram 43k

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No, I work with him. He can not reply to you because he spent all messages per day

ADD REPLY • link 4.8 years ago by adrian.pelaezl • 0

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I see. We will figure out if it is possible to remove this comment limit restriction.

By the way, if you've been up-voting his post and comments, please understand that such upvoting is not encouraged. Upvotes are for content with inherent objective value only, and almost none of apl0028's post/comments seem to have that value. In case such upvotes were given out, please go back and undo them.