Thanks very much for your help, will try to modify this!
Agathe
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bcftools merge, error "Could not parse the region(s)"
Hi all,
I am trying to merge multiple vcf files using bcftools version 1.6. Unfortunately, I receive the following error for all of my "chromosomes":
[E::_regions_init_string] Could not parse the region(s): chr1
ex:
[E::_regions_init_string] Could not parse the region(s): JA218_chr6:29940123..29944556_UTR-0_lenght=4434
[E::_regions_init_string] Could not parse the region(s): JA455_chr11:20047638..20052236_UTR-0_lenght=4599
[E::_regions_init_string] Could not parse the region(s): JA327_chr9:10804606..10807219_UTR-0_lenght=2614
[E::_regions_init_string] Could not parse the region(s): JA205_chr6:24945965..24949792_UTR-0_lenght=3828
I have using the following command:
bcftools merge file1.vcf.gz file2.vcf.gz file3.vcf.gz -o outfile -O v -0
My vcf files have been compressed with bgzip and indexed with tabix (also version 1.6) using:
bgzip file1.vcf; tabix -p vcf file1.vcf.gz
Not sure what is happening here. Any help would be appreciated and please, let me know if you need any additional piece of information.
Thanks very much,
Agathe
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Pierre Lindenbaum
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agathejouet •
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1 answer
from the VCF specification : https://samtools.github.io/hts-specs/VCFv4.3.pdf
CHROM - chromosome:(...) . The colon symbol (:) must be absent from all chromosome names to avoid parsing errors when dealing with breakends.
you vcf is not valid.
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I would go for something like:
awk -F '\t' '/^#/ {print;next;} {OFS="\t";gsub(/[\:\.\-]/,"_",$1);print;}' input.vcf
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please
you'd better always force bgzip/taxix and use a logical AND
The output is:
I have 759 "chromosomes" like this, in a similar format. Will also keep in mind to force overwrite and use the && (which I actually do in my rake file).
but is there the only whole word 'chr1' as you said in your first warning message ?