Hi,
I have a .txt file that contains only chromosomes and base positions. I have to convert it to "real" .vcf file with ref and alt allele and all the other columns so it could be suitable for other analyses. Concretely for GATK's Select Variants. Does anyone know how to do this? Is this possible?
The file looks like this: Chr1:12345678
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written
by
am29 •
2 answers
generate a VCF, without ALT.
awk -F ':' 'BEGIN{printf("##fileformat=VCFv4.2\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n");} {printf("%s\t%s\t.\tN\t.\t.\t.\t.\n",$1,$2);}' your.file.txt> tmp.vcf
bcftools reheader -f ref.fasta.fai tmp.vcf | bcftools norm --fasta-ref ref.fasta --check-ref e > new.vcf
You can create a VCF file in a programmatic way with libraries like
https://brentp.github.io/cyvcf2/writing.html
or
https://pyvcf.readthedocs.io/en/latest/index.html
but it would be a fairly complex task in my opinion.
A workaround could be to simulate reads from a mutated genome that has your variants applied, then call variants on that.
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