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Hi Giulio / All,
I tried to get +liftover going on our systems but found location of a couple of files needs to be detailed -- could anybody point to me?
They are 1kGP_high_coverage_Illumina.sit…
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What is the output supposed to look like?
I have a bcf.gz file that I ran hoping to calculate distances between 347 individuals. I do not think the documentation is super clear, so I ran it like th…
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Hi,
I'm trying to phase rare variants, which goes well for the greatest part. I used the files and instructions you provided in the [documentation](https://odelaneau.github.io/shapeit5/docs/tutoria…
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Let's say I generate a minimal VCF file:
```
echo -e "##fileformat=VCFv4.2
##contig=
#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO
20\t1\t.\tA\tC\t0\t.\t." > test.vcf
```
And let's say I crea…
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```
bcftools view --no-header ${vcf} | cut -f7 | sort | uniq -c
[W::bcf_hrec_check] Invalid tag name: "0START"
[W::bcf_hrec_check] Invalid tag name: "0END"
[W::vcf_parse_filter] FILTER 'SD' is not…
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Dear BCF(Tools) developers,
We are happy users of (BCF)Tools for storing and querying whole genome sequencing variant tables of a few hundred to few thousand samples.
File size and query perfo…
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### Need
As a user, I want clear outputs. At the moment variant files are a mix of vcf and bcf, some indexed and some not, some compressed and some not.
### Suggested approach
Standardise output va…
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Shapeit4 gave me an error on one chromosome:
> ERROR: Could not find conditioning haplotypes for [sample_137739] / check options --pbwt-* and --ibd2-*
` shapeit4 --input DNA.phased.chr3.bcf --ma…
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I installed BCF Forum in wordpress then found the link to the bimserver and bcfserver credentials.
I don't know what are the bcfserver credentials, are they the ones I use to access wordpress ?
…