I'm having trouble getting a first test run working with amrtester. I'm working on GRCh38. I have a bed file of test regions and a bam produced by bwa-meth. I am having trouble setting the required -chrom argument correctly. So far I've tried submitting the reference fasta, the fai, the output from fetchChromSizes hg38, and just the string 'hg38', but the output I get in all cases is the following:
NUMBER OF REGIONS: 31448
no chrom file for:
chr1 28735 29737 CPGI 0 +
Do you have a small working demo of this tool to illustrate the expected format?
I'm having trouble getting a first test run working with
amrtester. I'm working on GRCh38. I have a bed file of test regions and a bam produced by bwa-meth. I am having trouble setting the required-chromargument correctly. So far I've tried submitting the reference fasta, the fai, the output fromfetchChromSizes hg38, and just the string 'hg38', but the output I get in all cases is the following:Do you have a small working demo of this tool to illustrate the expected format?