fix mentioned in #933 isn't working for 23andme skipping rows for NCBI reference

[stereotypy]

Hi there, I was having the same problem in #933 and the fix below isn't working from the files from NCBI here: https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25/

Both specifying the column orientation and making the CHROM identifiers the same b/t 23andme file and the ref.fa solved the issue

Make "chr" absent ref.fa cat GRCh37.p13.genome.fa | sed 's/>chr/>/g' > GRCh37.23andme.fa

Specify column order for bcftools convert bcftools convert -c ID,CHROM,POS,AA --tsv2vcf genome_p1.txt -f GRCh37.23andme.fa -s genomeP1 -Oz -o genomeP1.vcf.gz

Thanks!

I also tried indexing it with samtools faidx as suggested in #1076 but it's still skipping everything.

The fix for now for me was using Ensembl's data here: ftp://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz

I am new to this and don't know enough about the format issues in fasta files to understand why this is happening but a quick peek at the headers looks a bit different between NCBI and Ensembl. It would be cool to have something built into bcftools that could maybe put a flag for what type of reference data you're working with to avoid these problems.

[pd3]

Since you are not showing any data, it is impossible to tell what went wrong. The issues you reference give some useful tips, not sure how to help more here.