Closed wodanaz closed 6 years ago
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.
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
Apparently there was a problem with the conversion. What does your input look like?
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
Your fasta has the chr
prefix for the chromosome name, while it looks like your tab file does not.
It worked, thank you so much.
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