Make fasta file from SNPs in two vcf files
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0
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6.1 years ago
sun.nation ▴ 120

Hello,

I have two vcf files with SNPs compared to same reference.

Vcf1:

Position SNP

1             A

3             T

6             G

8             C

Vcf2:

2            C

6            A

8            T

10          T

There are 6 different positions, I want to make fasta files for both vcf files. N for no data.

>Vcf1

ANTGCN

>Vcf2

NCNATT

Is there any helpful tools or scripts?

Thanks in advance

SS 

 

 

vcf fasta SNP phylogenetic Forum • 3.9k views
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6.1 years ago
Brice Sarver ★ 3.7k

If you have a true VCF, vcf-tab-to-fasta.pl is one of the easiest ways to convert to a fasta sequence. You convert to a tab-delimited format first, then run the perl script. You can also convert to fasta with invariant reference bases using GATK's FastaAlternateReferenceMaker.

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Thanks Brice, This worked good.

I was wondering if I can filter based on missing data. eg if 50% sample has missing SNP in a particular position- remove that position.

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1
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6.1 years ago

Whats about the R package PopGenome,

readData(, format="VCF")

region.as.fasta(...,type=1)

Best,

Bastian

 

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6.1 years ago

You can use the pyfaidx package for this. The VCF files should be tabix indexed:

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I was not able to figure out how to use the script. I know less about python. Can this be used with UNIX commands after installing? Please let me know, I will try.

Thanks

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No, if you're looking for something that is ready to run you're better off with brice's solution. Glad you found something that works!

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