Hello,
I have two .vcf files containing annotated SNP lists obtained from SNPeff for two different isolates of tubercle bacilli. I now wish to compare SNP differences between these two isolates. I wonder if there are any tools that I can use to perform the task.
Creates intersections, unions and complements of VCF files. Depending
on the options, the program can output records from one (or more)
files which have (or do not have) corresponding records with the same
position in the other files.
Compares positions in two or more VCF files and outputs the numbers of
positions contained in one but not the other files; two but not the
other files, etc, which comes handy when generating Venn diagrams. The
script also computes numbers such as nonreference discordance rates
(including multiallelic sites), compares actual sequence (useful when
comparing indels), etc.
bcftools stats [OPTIONS] A.vcf.gz [B.vcf.gz]
Parses VCF or BCF and produces text file stats which is suitable for
machine processing and can be plotted using plot-vcfstats. When two
files are given, the program generates separate stats for intersection
and the complements. By default only sites are compared, -s/-S must
given to include also sample columns. When one VCF file is specified
on the command line, then stats by non-reference allele frequency,
depth distribution, stats by quality and per-sample counts, singleton
stats, etc. are printed. When two VCF files are given, then stats such
as concordance (Genotype concordance by non-reference allele
frequency, Genotype concordance by sample, Non-Reference Discordance)
and correlation are also printed. Per-site discordance (PSD) is also
printed in --verbose mode.
Hello sanjay.bpkihs,
"compare" is such an elastic word. Could you please explain in detail how your output should look like?
fin swimmer