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  • Bcftools stats

    Hi everyone,

    I'm studying how to use bcftools and playing a little bit with its parameters to better understand what they really do. I did two tests on the same paired-end bam file, one with base quality 20 and the other with 2 minimum reads for a site and used bcftools stats to compare them (output bellow).

    My question is; does anyone know where can I find some documentation about this output and how it is done? I thought the "2" id was refering to the intersection between the two files, but when I look at the number of SNPs found (22393 for Q20, 275806 for m2 and 1764922 for both) it doesn't make any sense: the third number is bigger than the other two and it doesn't correspond to the union either.

    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.uQ20.vcf.bgzip S37.um2.vcf.bgzip
    #
    # Definition of sets:
    # ID [2]id [3]tab-separated file names
    ID 0 S37.uQ20.vcf.bgzip
    ID 1 S37.um2.vcf.bgzip
    ID 2 S37.uQ20.vcf.bgzip S37.um2.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: 388196
    SN 0 number of SNPs: 22393
    SN 0 number of MNPs: 0
    SN 0 number of indels: 112390
    SN 0 number of others: 0
    SN 0 number of multiallelic sites: 22439
    SN 0 number of multiallelic SNP sites: 22393
    SN 1 number of records: 277113
    SN 1 number of SNPs: 275806
    SN 1 number of MNPs: 0
    SN 1 number of indels: 1307
    SN 1 number of others: 0
    SN 1 number of multiallelic sites: 276058
    SN 1 number of multiallelic SNP sites: 275806
    SN 2 number of records: 257769020
    SN 2 number of SNPs: 1764922
    SN 2 number of MNPs: 0
    SN 2 number of indels: 38776
    SN 2 number of others: 0
    SN 2 number of multiallelic sites: 1773536
    SN 2 number of multiallelic SNP sites: 1764922

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