GBS VCF output files

[Dr Mathavan M]

Hi there

I have some queries in the output files of Tassel, In total I have 198 samples, I performed till VCF file generation. The output of productioHapMap_mseI.bcfstats.txt showed only 113 files, the output shown below,

 Definition of sets:
# ID    [2]id   [3]tab-separated file names
ID      0       productioHapMap_mseI.vcf.gz
# SN, Summary numbers:
#   number of records   .. number of data rows in the VCF
#   number of no-ALTs   .. reference-only sites, ALT is either "." or identical to REF
#   number of SNPs      .. number of rows with a SNP
#   number of MNPs      .. number of rows with a MNP, such as CC>TT
#   number of indels    .. number of rows with an indel
#   number of others    .. number of rows with other type, for example a symbolic allele or
#                          a complex substitution, such as ACT>TCGA
#   number of multiallelic sites     .. number of rows with multiple alternate alleles
#   number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
#
#   Note that rows containing multiple types will be counted multiple times, in each
#   counter. For example, a row with a SNP and an indel increments both the SNP and
#   the indel counter.
#
# SN    [2]id   [3]key  [4]value
SN      0       number of samples:      113
SN      0       number of records:      44199
SN      0       number of no-ALTs:      24462
SN      0       number of SNPs: 19734
SN      0       number of MNPs: 0
SN      0       number of indels:       9
SN      0       number of others:       0
SN      0       number of multiallelic sites:   36
SN      0       number of multiallelic SNP sites:       30

While checking the file fakebarcode.tsv

In total 198, 113 reads has good read count rest have few counts

pl check the attached file