Make fasta file from SNPs in two vcf files

Question

[sun.nation]

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

Answer 1

[Brice Sarver]

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.

[sun.nation]

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.

Answer 2

[bastianxpfeifer]

Whats about the R package PopGenome,

readData(, format="VCF")
region.as.fasta(...,type=1)

Best,
Bastian

Answer 3

[Matt Shirley]

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

[sun.nation]

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

[Matt Shirley]

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!