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Hi Jonathon,
When merging the dose files from MIS, the imputed site lists are guaranteed to be the same as long as no R2 filters are applied because MIS outputs even quasi-monomorphic variants. How…
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Given a multisample VCF file with different samples, if the sample name is given as a external variable, such as
`sample_name="NA00001" `
` zcat MULTI_VCF | vawk -v ext_var=$sample_name '{prin…
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Hello,
Can you please provide some more details on the format of graphtyper output VCF? I'm interested essentially in 2 points:
1. Variants definitions. Take the following example:
Given my me…
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If vcf looked for a $VCF_FILE envar, then the source-file/folder could be omitted.
./vcf.sh jane ~/contacts/*.vcf
becomes (after putting it in the $PATH)
vcf jane
Other *.vcf files/folders cou…
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Hi, I used the provided wget command to download the GRCh38 vcf file, but the file that installed was only 2KB and was just the following text saved into a file:
```
Google Drive can't scan this f…
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Hi Melanie,
Thanks for developing such amazing tool!
I encountered a problem when I want to view the vcf file using IGV or JBrowse, where we have to zip and index the vcf file prior to viewing. I…
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Hello, I ran "selscan --xpehh --vcf vcf1_Chr1.gz --vcf-ref vcf2_Chr2.gz --pmap --out outfile", but no files were generated.
The result of the operation is:
selscan v1.3.0
Opening vcf1_Chr1.gz...
L…
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Hi eveyone,
I want to verify the best donor numbers of my vcf-data,which is the outputs of cellsnp-lite. I tried the demo command developers provided as follows:
`cell_vcf = vireoSNP.load_VCF('ba…
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I am currently doing benchmarking of the VCF files with the gold standard file **HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_PGandRTGphasetransfer.vcf**. Whil…
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Hi Michael,
Thanks for such a useful script. I am trying to convert a vcf file that has both modern and ancient samples and the script is working fine when I am using parameters (-q 30 -y 5 -x 90 -s)…