5.5 years ago by

New Zealand

RTG Tools includes a `vcfstats`

command that outputs basic statistics for every sample (or you can request specific samples). e.g. on a small simulated vcf:

$ rtg vcfstats family.vcf.gz
Location : family.vcf.gz
Failed Filters : 0
Passed Filters : 144
Sample Name: sm_mom
SNPs : 91
MNPs : 1
Insertions : 5
Deletions : 2
Indels : 0
Same as reference : 1
Missing Genotype : 44
SNP Transitions/Transversions: 1.74 (73/42)
Total Het/Hom ratio : 2.96 (74/25)
SNP Het/Hom ratio : 2.79 (67/24)
MNP Het/Hom ratio : - (1/0)
Insertion Het/Hom ratio : 4.00 (4/1)
Deletion Het/Hom ratio : - (2/0)
Indel Het/Hom ratio : - (0/0)
Insertion/Deletion ratio : 2.50 (5/2)
Indel/SNP+MNP ratio : 0.08 (7/92)
Sample Name: sm_dad
SNPs : 73
MNPs : 2
Insertions : 2
Deletions : 3
Indels : 0
Same as reference : 1
Missing Genotype : 63
SNP Transitions/Transversions: 1.87 (58/31)
Total Haploid : 19
Haploid SNPs : 17
Haploid MNPs : 0
Haploid Insertions : 1
Haploid Deletions : 1
Haploid Indels : 0
Total Het/Hom ratio : 2.59 (44/17)
SNP Het/Hom ratio : 2.50 (40/16)
MNP Het/Hom ratio : 1.00 (1/1)
Insertion Het/Hom ratio : - (1/0)
Deletion Het/Hom ratio : - (2/0)
Indel Het/Hom ratio : - (0/0)
Insertion/Deletion ratio : 0.67 (2/3)
Indel/SNP+MNP ratio : 0.07 (5/75)
[...]

most people write their own script to parse data like that in a VCF file.

2.4kUse NextGene software trial 35 days

200My lab is using the NextGene free trial and we have managed to align the sequencing run and can see the variants on screen. Hovering over the variant, we see the specific data. However, we cannot get the report that lists all the variants detected with the variant frequency, coverage, etc. Can anybody help? How do we achieve the report?? Thanks

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