Problems with convert example

[wodanaz]

I feel like I am missing something with the example described in https://samtools.github.io/bcftools/howtos/convert.html. I think it doesn't work for me because I don't have a SampleName list file. Can you elaborate and describe this file please according to the raw data from 23andme.

Thank you

[pd3]

SampleName in the example is not a file, but a string - a sample name. Conversion to a single-sample VCF is supported at the moment.

[wodanaz]

Great, thanks for your answer. I am running a conversion of the 23andme output ( only for chromosome 1) to vcf file and this is the screen result.

Rows total: 77016 Rows skipped: 77016 Missing GTs: 0 Hom RR: 0 Het RA: 0 Hom AA: 0 Het AA: 0

[pd3]

Apparently there was a problem with the conversion. What does your input look like?

[wodanaz]

Ok, let me show you my command line:

bcftools convert --tsv2vcf chr1.input.tab -f chr1.fa -s ind1 -Ob -o ind1.bcf and these are the results:

Rows total: 77016 Rows skipped: 77016 Missing GTs: 0 Hom RR: 0 Het RA: 0 Hom AA: 0 Het AA: 0

head chr1.input.tab

rs4477212 1 82154 AA rs3094315 1 752566 AG rs3131972 1 752721 AG rs12124819 1 776546 AA rs11240777 1 798959 AA

The header of hg19 chromosome 1 head chr1.fa

chr1 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Thanks for your help

[mcshane]

Your fasta has the chr prefix for the chromosome name, while it looks like your tab file does not.

[wodanaz]

It worked, thank you so much.