You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Hi, I recently ran a bacterial sample (nanopore sequenced) through Clair CallVarBam to find variants in a gyrA gene. I used the --haploid flag and the resulting vcf file is shown below. My question is why the genotype (GT) is still reported as 1/1 (suggesting diploidity, no?) instead of only 1? Maybe I misunderstand how the genoype is reported or that the data has evidence that suggests diploidity. Thanks in advance.
##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=LowQual,Description="Confidence in this variant being real is below calling threshold.">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=INS,Description="Insertion of novel sequence">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=LENGUESS,Number=.,Type=Integer,Description="Best guess of the indel length">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=AF,Number=1,Type=Float,Description="Estimated allele frequency in the range (0,1)">
##contig=<ID=gyrA>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
gyrA 262 . G A 1015 . . GT:GQ:DP:AF 1/1:1015:188:0.7713
gyrA 491 . T TC 516 . . GT:GQ:DP:AF 1/1:516:188:0.1596
The text was updated successfully, but these errors were encountered:
Hi, I recently ran a bacterial sample (nanopore sequenced) through Clair CallVarBam to find variants in a gyrA gene. I used the --haploid flag and the resulting vcf file is shown below. My question is why the genotype (GT) is still reported as 1/1 (suggesting diploidity, no?) instead of only 1? Maybe I misunderstand how the genoype is reported or that the data has evidence that suggests diploidity. Thanks in advance.
##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=LowQual,Description="Confidence in this variant being real is below calling threshold.">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=INS,Description="Insertion of novel sequence">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=LENGUESS,Number=.,Type=Integer,Description="Best guess of the indel length">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=AF,Number=1,Type=Float,Description="Estimated allele frequency in the range (0,1)">
##contig=<ID=gyrA>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
gyrA 262 . G A 1015 . . GT:GQ:DP:AF 1/1:1015:188:0.7713
gyrA 491 . T TC 516 . . GT:GQ:DP:AF 1/1:516:188:0.1596
The text was updated successfully, but these errors were encountered: