Question: VCF/BCF File format QS score in INFO header
1
gravatar for ga32huv
2.3 years ago by
ga32huv10
ga32huv10 wrote:

Hi everyone,

After calling samtools mpileup my file header looks like this:

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##samtoolsVersion=1.3.1+htslib-1.3.1
##ALT=<ID=*,Description="Represents allele(s) other than observed.">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">

I did not find a suitable documentation that explains comprehensive the INFO header. I am looking to understand more the QS (Auxiliary tag used for calling) score. Is there a correlation between QS und PL?

Example:

chrom   pos alt ref QUAL    PL:DP   DP  QS  VDB SGB RPB MQB MQBS    BQB

chr1    6579653 G   C,A,T   0   245,0,255,255,255,255,255,255,255,255:798   798 0.732312,0.264416,0.00255397,0.000718305    1,13E-08    -0,693147   0,161204    1   1   0,999199

I would be very greateful for every information I can get. Maybe I overlooked something, but this are the main links where I'ved searched for an answer.

http://samtools.sourceforge.net/mpileup.shtml

https://samtools.github.io/hts-specs/VCFv4.2.pdf

https://cseweb.ucsd.edu/classes/sp16/cse182-a/notes/VCFv4.2.pdf

Thank you very much.

snp • 1.6k views
ADD COMMENTlink written 2.3 years ago by ga32huv10

I have the exact same question. Can't find an answer anywhere and have no idea why this hasn't been answered!

ADD REPLYlink written 3 months ago by tbb2110
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