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?
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anasjamshed
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
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?
use bcftools merge in the next step to merge different samples, or bcftools concat to concatenate when the samples are the same
ok . how can I use snp2hla tool for impuation based on vcf files
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
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