Online service for fastq and BAM conversion

[vbnetkhio]

It is also possible to download vcf and convert using plink. But maybe this kind of vcf needs additional processing before?

i use Dnakitstudio because it can convert vcf directly to 23andme. But it should work in plink too.

[Lucas]

i use Dnakitstudio because it can convert vcf directly to 23andme. But it should work in plink too.

Yes I forget about it

[smd555]

There is probably something wrong with your .dat file, could you post the first few lines from it?

Do you mean my "filter.txt" file, which I have made from "Template_23andme_v3"? This is how its beginning looks like in Excel:

[Lucas]

Generally good practise is not to use excel for opening genome files in Windows, especially when you want to save it but text editor which can open large files quickly like Edit Pad. It also does not change formatting / encoding like standard notepad.

[smd555]

Generally good practise is not to use excel for opening genome files in Windows, especially when you want to save it but text editor which can open large files quickly like Edit Pad. It also does not change formatting / encoding like standard notepad.

Did you try that bcftools filter? I wonder what is wrong - this tool, or my filter file, or my settings, or the input bcf files?

[smd555]

The other problem is that some .bcf cannot be compressed to more small .bcf using bcftools call - there is not error, but the resulting .bcf is empty

Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid

[vbnetkhio]

Do you mean my "filter.txt" file, which I have made from "Template_23andme_v3"? This is how its beginning looks like in Excel:

i found the problem. chromosomes should be named like chr1, chr2 ... chrY.
MT should probably be excluded.

here's the file:

https://easyupload.io/vwenmx

you should use it in the "bcftools mpileup" step already. (restrict to>regions>history dataset)
it wil finish much faster and the output file will be smaller. after that it's not neccesary to filter anymore, just run bcftools call and you have your file.

[smd555]

i found the problem. chromosomes should be named like chr1, chr2 ... chrY.
MT should probably be excluded.

here's the file:

https://easyupload.io/vwenmx

you should use it in the "bcftools mpileup" step already. (restrict to>regions>history dataset)
it wil finish much faster and the output file will be smaller. after that it's not neccesary to filter anymore, just run bcftools call and you have your file.

Thank you very much! This filter works. Unfortunately I have many problems with files from European Nucleotide Archive. It will take some time to check all the nuances with filtering.

[smd555]

I have a question - on the Vahaduo there are samples of the Sredniy Stog I4110_Ukraine_EN and I5882_Ukraine_EN Did they come from here?:https://www.ebi.ac.uk/ena/browser/vi...652?show=reads
Their files from ENA generate empty VCFs.

[vbnetkhio]

I have a question - on the Vahaduo there are samples of the Sredniy Stog I4110_Ukraine_EN and I5882_Ukraine_EN Did they come from here?:https://www.ebi.ac.uk/ena/browser/vi...652?show=reads
Their files from ENA generate empty VCFs.

bam or vcf files? with filtering or without?

try without filtering, or with a different version of the genotype build (for example hg_g1k_v37 instead of the normal hg19) and try with both kinds of filter (chr1, chr2 or 1,2..)