setting parameters for Novoalign 2-6 bp insertions deletions

[12jrowley2]

I am looking for insertions 2-6 bp in length in the native novoalign output - but see that novoalign did not output any insertions greater than 1 bp. Am I looking for this wrong?

awk '$14 ~ /\+([AGTC]){2,}/ { print $0}'
None found
awk '$14 ~ /\+([AGTC])/ { print $0}'
Lots found

these are the changed parameters used in novoalign with 50 bp single end illumina reads:

-p '-F ILMFQ -t60 -r0.2 -q5' -l -w 24 -k 1 -t -o kaplan-em

am I missing them with these parameters?

thanks for any input!

[sparks]

This works...

awk '$14 ~ /\+([AGTC][ACGT])/ { print $0}'

[SNPsaurus]

I think your -t parameter is too low. According to http://www.novocraft.com/wiki/tiki-i...gnment+Scoring there is a gap opening penalty of 45 and 10 for each base. Given normal quality scores those penalties would pass above -t60. And any additional mismatches would make it worse. Is there a reason you chose a low -t parameter? Just get rid of it to use the default if there is no particular reason. A threshold of 140 would allow a 6 bp indel plus one other mismatch (or seq error).