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
-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 id 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 id key 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