Recommended -c setting

[gevro]

Hi, In a prior version, you said that you keep -c the same for both var and indel steps, and that you run it with -c 0, in issue: #50

However, the default settings in the var and indel programs is -c 0.02.

Which setting is more stringent (i.e. removes more false positives): -c 0 or -c 0.02? And what do you recommend we use? Is -c 0 ok for both var and indel, especially considering our recent finding of some indel artifacts on NovaseqX?

Thanks!

[gevro]

Just to add, so far we have been using -c 0 for both var and indel.

[fa8sanger]

-c 0.02 is less stringent, it allows up to 2% of reads with soft-clipping This parameter usually doesn’t have much impact

On 30 Dec 2023, at 21:54, gevro @.***> wrote:

Hi, In a prior version, you said that you keep -c the same for both var and indel steps, and that you run it with -c 0, in issue: #50 [github.com]https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cancerit_NanoSeq_issues_50&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=v9-R7fUmjpv-9Zaqyk1nlnlOC3qPkTEJz5tyYxg2uec&m=CDgzkSfRp8QUO0IYmRw5fef68PaW0Mb0cqQo_Kb_2op8sVzyWaFkH7fUSlXT_g7g&s=TSTF5zhs5tk-gh3Oot25BJAxZMMI9gLsQjqC4YaDbAo&e=

However, the default settings in the var and indel programs is -c 0.02.

Which setting is more stringent (i.e. removes more false positives): -c 0 or -c 0.02? And what do you recommend we use? Is -c 0 ok for both var and indel, especially considering our recent finding of some indel artifacts on NovaseqX?

Thanks!

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