ChenDepp

@brentp thanks for your reply, I had solved the problem , good luck. i hava an another question about the five file *.disc.bam, *.disc.bam.orig.bam, *.histo, *.split.bam, *.split.bam.orig.bam. the first question...

@christian-lanius Thanks you, I will dissect the mm_idx_load and mm_idx_dump functions, But i am not good at C language， If you can provide the corresponding python code，will save me a...

hi when i running partition step, find it can't get result. The report message is as follows: 

@lidaof hi thanks you very much.

> Hi @ChenDepp > This is probably an error with HTSJDK's CSI decoder for BAM files. Can you reindex your bam file with BAI index and try again. Looks like...

> Hmn, we might have an off by one error somewhere... @lbergelson hi，Are you saying it's gatk's problem, or is it my problem when dealing with the file?

hi @gokalpcelik I used GenomicsDBImport to replace CombinedGVCFs, but it has new problems, GenotypeGVCFs for GenomicsDB is so slow, can only get 900K interval vcf in 9 hours. how can...

when i running vg surject convert gam to bam, it report warnning information as below  Is this the reason why gatk cannot run successfully?

@adamnovak As you said, the chromosome names of the pan-genome are chr1、chr2. so the problem may be that gatk can't accept the bam converted by vg-surject. Thank you for your...

@adamnovak I have another question. A sample has 35016715 paired-end reads, but using vg stat to analyze the gam file gives the following information:  there hava 37157187 reads，how to...