Hello everyone,

I'm studying the parameters of bcftools view and trying to understand them better, so I've done two tests, one with bcftools -c only and the other with bcftools -e only and compared them with bcftools stats (results bellow).

I've read on the manual that the -c option forces the -e option. My question is, if one forces another, the number of SNPs in common shouldn't be higher? I understand that there are many SNPs called only by the -e option, but shouldn't all the SNPs called by the -c option be present in the -e as well?

Does anyone know where could I find a good documentation about how the -c and -e options work?

Thanks in advance!

# This file was produced by bcftools stats (1.2+htslib-1.2.1) and can be plotted using plot-vcfstats.
# The command line was:    bcftools stats  S37.um2Q20.c.vcf.bgzip S37.um2Q20.e.vcf.bgzip
#
# Definition of sets:
# ID    [2]id    [3]tab-separated file names
ID    0    S37.um2Q20.c.vcf.bgzip
ID    1    S37.um2Q20.e.vcf.bgzip
ID    2    S37.um2Q20.c.vcf.bgzip    S37.um2Q20.e.vcf.bgzip
# SN, Summary numbers:
# SN    [2]id    [3]key    [4]value
SN    0    number of samples:    1
SN    1    number of samples:    1
SN    0    number of records:    258033024
SN    0    number of SNPs:    691841
SN    0    number of MNPs:    0
SN    0    number of indels:    3020
SN    0    number of others:    0
SN    0    number of multiallelic sites:    4872
SN    0    number of multiallelic SNP sites:    4694
SN    1    number of records:    212276037
SN    1    number of SNPs:    1454264
SN    1    number of MNPs:    0
SN    1    number of indels:    20454
SN    1    number of others:    0
SN    1    number of multiallelic sites:    1460927
SN    1    number of multiallelic SNP sites:    1454264
SN    2    number of records:    12043
SN    2    number of SNPs:    115
SN    2    number of MNPs:    0
SN    2    number of indels:    11928
SN    2    number of others:    0
SN    2    number of multiallelic sites:    677
SN    2    number of multiallelic SNP sites:    115