Pindel Is Not Detecting Long Insertions

Question

[roalva1]

Hello,

I am using pindel to detect long insertions, but it doesn't detect anything in any of my samples. However it detects inversions when I say to it not to put it. Why could be this? I called it in 250 samples where I know there are long insertions.

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./pindel -f $ref -i $inputfile -o $output  --report_interchromosomal_events false --report_duplications false --report_inversions false

is there any other software a part from breakdancer and pindel to detect long insertions?

Best regards

Answer 1

[liangkaiye]

how long are your insertions and what is the read length? Pindel finds insertions with maximum length of ReadLength - 20, if it needs some bases to align to the reference. if you do not need breakpoints and the sequence inserted, read-pair approaches like breakdancer is the choice. but again, there is maximum size limit for insertions detected by read-pair approach as two reads in a pair must span the insertion: InsertSize - 2 * ReadLength.

you will need local assembly if your insertion is longer than the read length.