bam.snp.candidate.out problem

[KseniaJuravel]

Hi, I am using the BS-Snper on bismark output.

My command is:
perl BS-Snper/BS-Snper.pl
--fa $REF $i
--output $i.snp.candidate.out --methcg $i.meth.cg
--methchg $i.meth.chg --methchh $i.meth.chh
--minhetfreq 0.1 --minhomfreq 0.85 --minquali 15
--mincover 10 --maxcover 1000 --minread2 2
--errorate 0.02 --mapvalue 20 > $i.vcf

The tool works great!!!
But
My output for the SNPs looks weird; the headers do not fit the output column number.

Do you have any idea why?

The file looked like this:

head ../ChP_output/temp_20241223/BS_Snper_Output_ChP/NW_017553014.1.bam.snp.candidate.out
#CHROM POS ID REF ALT QUAL FILTER GENOTYPE FREQUENCY Number_of_watson[A,T,C,G] Number_of_crick[A,T,C,G] Mean_Quality_of_Watson[A,T,C,G] Mean_Quality_of_Crick[A,T,C,G]
NW_017553014.1 151 A 6,0,0,1 9,0,0,0 37,0,0,37 37,0,0,0 37 40
NW_017553014.1 271 C 0,0,2,0 2,0,1,0 0,0,37,0 37,0,37,0 42 42
NW_017553014.1 281 C 0,0,5,0 1,0,2,0 0,0,37,0 37,0,37,0 42 42
NW_017553014.1 282 C 0,0,5,0 0,1,2,0 0,0,37,0 0,37,37,0 42 42
NW_017553014.1 405 A 6,0,0,1 9,0,0,0 37,0,0,25 37,0,0,0 40 39
NW_017553014.1 441 T 0,4,0,0 0,8,1,0 0,37,0,0 0,37,37,0 39 39
NW_017553014.1 530 T 0,1,0,0 0,1,1,0 0,37,0,0 0,37,37,0 30 36
NW_017553014.1 639 G 1,0,0,1 0,0,0,4 25,0,0,37 0,0,0,34 37 36
NW_017553014.1 745 T 0,6,0,0 0,8,1,0 0,37,0,0 0,37,25,0 39 39

Could you please provide some rules of thumb or guidelines on how the tool addresses SNP counting compared to GATK?

Thank you!