-
Notifications
You must be signed in to change notification settings - Fork 20
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Genotype outputs all sites #142
Comments
I found the problem, REF and ALT in --vcf cannot be the same, graphtyper will ignore sites where REF and ALT are the same. POS REF ALT #CHROM ID QUAL FILTER INFO
1 G A chrM . 0 . .
1 G T chrM . 0 . .
1 G C chrM . 0 . .
2 A G chrM . 0 . .
2 A T chrM . 0 . .
2 A C chrM . 0 . . For others’ reference |
Hey, this will create a graph where every read maps at every position perfectly. I guess you want to get read counts for each base? I'd suggest using samtools mpileup. Best, |
Thanks for the reply, I am testing this software |
When using default parameters for both tools, GraphTyper calls out approximately 19,000 variants with only NA12878 (1000 Genomes) as input, while GATK calls out over 40,000. Is this normal? |
Can graphtyper output the genotyping of all sites in a region, such as mitochondrial 16569bp?
I tried this command but the resulting vcf file does not have any site information in it.
output_chrM.vcf.modif.gz like:
The text was updated successfully, but these errors were encountered: