I have 3 following questions about VCF output given by SAMtools/bcftools
Q1 How are QUAL field values calculated?
SAMtools manual gives QUAL definition "Phred Scaled probability of all
samples being homozygous reference". Whereas the standard VCF 4.1
(from 1000 Genomes) states it as -10log_10(call in ALT is wrong). Does
QUAL from SAMtools means -10log_10(REF call in ALT is wrong)?
Q2 How is GQ(genotype quality) is calculated by SAMTools and how it is
different from QUAL?
Q3 ALT field and genotype do not correspond in case of more than 1 ALT
allele is mentioned. For example
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
chr1 1254136 . G A,C 18.3 .
Here ALT allele is A,C whereas Genotype is 1/1 (should have been 2/1
according to standard VCF format; a heterozygotic condition)
chr1 167973014 . C A,T 5.85 .
Here ALT allele is A,T whereas Genotype is 0/1
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