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Fixing tests

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JoseEspinosa 2021-02-02 09:57:55 +01:00
parent 382ea31e7e
commit c25f8f0f6c
3 changed files with 4 additions and 68 deletions
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output/bcftools/test.bcftools_stats.txt
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# This file was produced by bcftools stats (1.11+htslib-1.11) and can be plotted using plot-vcfstats.
# The command line was: bcftools stats test.vcf
#
# Definition of sets:
# ID [2]id [3]tab-separated file names
ID 0 test.vcf
# 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: 1
SN 0 number of records: 15
SN 0 number of no-ALTs: 2
SN 0 number of SNPs: 7
SN 0 number of MNPs: 0
SN 0 number of indels: 3
SN 0 number of others: 3
SN 0 number of multiallelic sites: 1
SN 0 number of multiallelic SNP sites: 1
# TSTV, transitions/transversions:
# TSTV [2]id [3]ts [4]tv [5]ts/tv [6]ts (1st ALT) [7]tv (1st ALT) [8]ts/tv (1st ALT)
TSTV 0 3 5 0.60 3 4 0.75
# SiS, Singleton stats:
# SiS [2]id [3]allele count [4]number of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consistent [9]repeat-inconsistent [10]not applicable
SiS 0 1 8 3 5 3 0 0 3
# AF, Stats by non-reference allele frequency:
# AF [2]id [3]allele frequency [4]number of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consistent [9]repeat-inconsistent [10]not applicable
AF 0 0.000000 8 3 5 3 0 0 3
# QUAL, Stats by quality:
# QUAL [2]id [3]Quality [4]number of SNPs [5]number of transitions (1st ALT) [6]number of transversions (1st ALT) [7]number of indels
QUAL 0 998 7 3 4 3
# IDD, InDel distribution:
# IDD [2]id [3]length (deletions negative) [4]number of sites [5]number of genotypes [6]mean VAF
IDD 0 -2 1 0 .
IDD 0 3 1 0 .
IDD 0 8 1 0 .
# ST, Substitution types:
# ST [2]id [3]type [4]count
ST 0 A>C 1
ST 0 A>G 0
ST 0 A>T 0
ST 0 C>A 2
ST 0 C>G 0
ST 0 C>T 1
ST 0 G>A 1
ST 0 G>C 0
ST 0 G>T 0
ST 0 T>A 2
ST 0 T>C 1
ST 0 T>G 0
# DP, Depth distribution
# DP [2]id [3]bin [4]number of genotypes [5]fraction of genotypes (%) [6]number of sites [7]fraction of sites (%)