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DecodeGenetics / graphtyper

Population-scale genotyping using pangenome graphs
http://dx.doi.org/10.1038/ng.3964
MIT License
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genotyping small variant error, result only contains vcf header! #135

Closed tanger-code closed 11 months ago

tanger-code commented 11 months ago

Hi, I want to genotyping the chr21 using command:graphtyper genotype GRCh38#chr21.fa --sam=chr21.sorted.bam --region=chr21. But there seems to be something wrong with it. The result only contains header. image

Why does this happen？The ref GRCh38#chr21.fa file that I used contains 2 lines.

hannespetur commented 11 months ago

Hey, can you check if the contig names match in the FASTA and BAM are chr21? Also were there any log messages?

tanger-code commented 11 months ago

This is the first 100 lines of the BAM file： chr21_bam_head100.txt And this is the first 100 lines of the ref.fa file: GRCh38_chr21_head100_fa.txt The contig name is both chr21. And there is no error log for GraphTyper.

Is there a problem with my bam file or fasta file?

hannespetur commented 11 months ago

Sorry, graphtyper won't work with long read data.