Pierre Lindenbaum

yes it's only for diploid. I wrote this program for diploid only. If you want to create a 'fake' diploid. in https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/VcfToBam.java#L288 change the lines: ``` if(alleles.size()!=2) throw new RuntimeException("Not...

I agree my tool is quite poor and is just too slow. I strongly suggest you use CNVNator https://github.com/abyzovlab/CNVnator

not tested but it should be something like this: ``` final String contig= "rotavirus"; final int delStart = 1044; final int delEnd = 1050; final char mutbase='T'; if(record.getReadUnmappedFlag()) return false;...

Sorry, I don't currently have any data at home to play with this. Try with a a one-read bam carrying a deletion and test various combinations.

you 'll have to loop for a cigarElement with CigarOperator.I

hi thanks for using this tool and thank you for submitting this issue. I wrote this mostly for fun. May I ask why do you use it instead of bcftools...

@fernanarr I think I found the bug. I recently rewrote a large part of this software but my test was too simple. The bug is here: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/calling/MiniCaller.java#L433 replace `+ new...

@gilhornung thank you for the bug report. The problem was caused by an unicode character in the code. I hope it's fixed now.

I posted the answer yesterday: https://www.biostars.org/p/458494/#458518

You can always add a fake genotype ``` wget -O - "https://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/00-All.vcf.gz" |\ gunzip -c |\ awk '/^#CHROM/ {printf("##FORMAT=\n%s\tFORMAT\tSAMPLE\n",$0);next} {printf("%s\tGT\t0/1\n",$0);}' ```