Genotype outputs all sites

[lihaicheng7003]

Can graphtyper output the genotyping of all sites in a region, such as mitochondrial 16569bp?

./graphtyper genotype ~/data1/References/human/Homo_sapiens_assembly38.fasta --sam=~/data1/project10/subdata/1.markdup.bam --region=chrM --output=~/data1/project19/results_chrM --vcf=output_chrM.vcf.modif.gz --force_no_filter_zero_qual

I tried this command but the resulting vcf file does not have any site information in it.
output_chrM.vcf.modif.gz like:

##fileformat=VCFv4.2
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
chrM    1       .       G       G       0       .       .
chrM    2       .       A       A       0       .       .

[lihaicheng7003]

I found the problem, REF and ALT in --vcf cannot be the same, graphtyper will ignore sites where REF and ALT are the same.
I manually made a vcf file for --vcf, so that all sites can be output

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

[hannespetur]

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,
Hannes

[lihaicheng7003]

Thanks for the reply, I am testing this software

[lihaicheng7003]

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?