Hi, I have been using bcftools stats, but I'm uncertain about what several fields in the output mean.
This is the output from vcftools stats on my file: # SN, Summary numbers: # SN [2]id [3]key [4]value SN 0 number of samples: 4301 SN 0 number of records: 803 SN 0 number of SNPs: 714 SN 0 number of MNPs: 0 SN 0 number of indels: 94 SN 0 number of others: 7 SN 0 number of multiallelic sites: 33 SN 0 number of multiallelic SNP sites: 2 Does "multiallelic" denote "more than 2 alleles" rather than "not monomorphic"? The number of SNPS+indels+others does not sum to the total number of records. Is this because an SNP can also be an indel or "other?" What types of variants are covered by "others" here? Why is the id[2] field blank for all sections of my output? Thanks, James Blackshaw
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