Skip to main content

Table 7 Homopolymeric sequences flanking false positive variants

From: GATK hard filtering: tunable parameters to improve variant calling for next generation sequencing targeted gene panel data

  Chr Position Flanking sequence N° of occurrences
HC dataset
Homo SNVs chr10 131565164 CCGGTTGGGGA 77
  chr3 178921420 GGACTGTTTTT 73
Het SNVs chr13 48919347 TAAACATTTTA 63
  chr3 178937372 CTTGGTAAAAG 9
Homo Indels chr4 55602995 AGAGCCAAAAA 1842
  chr10 89693016 AAGTTATTTTT 1802
Het Indels chr13 48955363 AGTTACTTTTT 2175
  chr3 178941853 CTATCCTTTTT 1678
LC dataset
Homo SNVs chr2 204736165 GGGTTGTTTTT 334
  chr13 48954225 GGTAAATTTTT 241
Het SNVs chr7 140534584 AAACAGAAAAA 32
  chr13 48955464 CTTTGATTTTT 20
Homo Indels chr7 140481508 AACAGTAAAAA 1153
  chr7 140481513 TAAAAAAGTCA 1084
Het Indels chr3 69915434 TAAAGGAAAAA 1202
  chr10 89693016 AAGTTATTTTT 1107
  1. Variant locus is on the 6th nucletide (bold) of the 11 nucleotide string (flanking sequence)