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
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written
by
sun.nation
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.
•
written
by
Brice Sarver
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.
•
written
by
sun.nation
Whats about the R package PopGenome,
readData(, format="VCF")
region.as.fasta(...,type=1)
Best,
Bastian
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written
by
bastianxpfeifer •
You can use the pyfaidx package for this. The VCF files should be tabix indexed:
•
written
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Matt Shirley
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
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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