Convert bcf to vcf and run snp2hla tool in windows subsytem for linux

Question

[anasjamshed]

i have 2 bcf files from chr 1 to chr 22 . I want to convert it to vcf and then use snp2hla tool to get the hla. I would like to use bcf tool for coversion. Is it possible through wsl for linux?

Answer 1

[Istvan Albert]

when you run bcftools you get the choice of the output via the -O flag

-O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]

simply a

 bcftools view -O v input.bcf > output.vcf

should suffice

[anasjamshed]

i convert the bcf to vcf by using:

for file in *.bcf; do
    bcftools view -O v -o "${file%.bcf}.vcf" "$file"
done

but I want to merge them all in one folder also I want to use snp2hla to get hla?

[Istvan Albert]

use bcftools merge in the next step to merge different samples, or bcftools concat to concatenate when the samples are the same

[anasjamshed]

ok . how can I use snp2hla tool for impuation based on vcf files

[Istvan Albert]

different questions need to go into their separate threads to keep the concepts isolated and focused on on topic

this thread is about converting bcf to vcf, if that step is successful but now you have new questions you need to open a new thread specifically about those