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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)