Empty output file after SNV calling using bayes method

[Relindis2018]

Hi, Dr Guo,

After running the following command cgmaptools snv -m bayes --bayes-dynamicP -i AK0H.ATCGmap.gz -v filename.VCF, I get an output file containing only header information as follows:

##fileformat=VCFv4.2
##fileDate=20230217
##source=CGmapTools
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=GU,Number=.,Type=String,Description="Genotype is Unidentified:R=A/G, Y=T/C">
##FILTER=<ID=q10,Description="Quality below 10">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001

I appreciate any help to resolve this problem.

Relindis

[guoweilong]

Have you fixed this issue? You can try to see if the command works with the test files ( under the folder cgmaptools/test/ ).