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I have an alignment with 140 reference reads (Ref Base = C) and 10 variant Reads (Var Base = T) at locus: Chr17:7578406. When I use the "EMIT_ALL_SITES" mode, the UnifiedGenotyper generates the following output:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT z 17 7578406 rs28934578 C A 0 LowQual AC=0;AF=0.00;AN=2;DB;DP=150;Dels=0.00;FS=0.000;HaplotypeScore=11.1188;MLEAC=0;MLEAF=0.00;MQ=38.26;MQ0=0 GT:AD:DP:GQ:PL 0/0:140,0:150:99:0,361,4503
My questions are:
1) In ALT column, why is the base "A" being shown? Is it a randomly selected base when no SNP is identified at that position?
2) The ID column shows dbSNP record rs28934578 which is a C>T mutation (which is what my data has). Why is the dbSNP records for C>T mutation in the output when no variant is identified at this position (or C>A variant is shown?). Does this imply that ID column shows ALL dbSNP records at that position rather than a dbSNP record of the identified variant?
3) Is there a document that details the VCF output when EMIT_ALL_VARIANTS is used so I could understand the output vcf?