vtools issueshttps://git.lumc.nl/klinische-genetica/capture-lumc/vtools/-/issues2019-04-18T14:09:33+02:00https://git.lumc.nl/klinische-genetica/capture-lumc/vtools/-/issues/3Average / median calculation of raw q scores2019-04-18T14:09:33+02:00Sander BollenAverage / median calculation of raw q scoresSee https://gigabaseorgigabyte.wordpress.com/2017/06/26/averaging-basecall-quality-scores-the-right-way/See https://gigabaseorgigabyte.wordpress.com/2017/06/26/averaging-basecall-quality-scores-the-right-way/SantcroosSantcrooshttps://git.lumc.nl/klinische-genetica/capture-lumc/vtools/-/issues/8Sites with different ALT alleles are dropped silently2019-12-16T11:15:21+01:00van den BergSites with different ALT alleles are dropped silentlyIf the same site in two vcf files have different ALT alleles, vtools-evaluate will silently ignore this position, even if the variants could be resolved. This is because it used cyvcf2 genotype codes where `0=homref`, `1=heterozygous`, `...If the same site in two vcf files have different ALT alleles, vtools-evaluate will silently ignore this position, even if the variants could be resolved. This is because it used cyvcf2 genotype codes where `0=homref`, `1=heterozygous`, `2=hom alt`, `3=no call`. These genotype codes only make sense when the ALT and REF alleles are identical.van den Bergvan den Berg