samtools for indel

[bair]

Hello all,

I used samtools to detect indel (aligned by bwa), which identified >1m indels, it's too much comparing with data in publications. Default setting used expect Q50.

The number of indel will drop sharply when RMS>50, the default setting is 10.

Does anyone know how to set the filter to get a reasonable number of indel? How do I know the maxmum length of indel? (bwa sampe does not have such option)

Many thanks!

[lh3]

try 0.1.10

[bair]

thank you lh3,

samtools pileup updated, samtools.pl seems not changed.

I'm running the new version, hope there is no big difference for snp calling since validation has done. Will focus on small size indel (<4 bp)

[lh3]

use mpileup+bcftools, not pileup. See the manual page.

[dawe]

try 0.1.10

Is it out?

[lh3]

You should sign up the [email protected] mailing list. It is extremely low traffic, about an email in a couple of months.

[dawe]

I will, thanks!

[drio]

Bair, let us know what differences you find when running samtools (0.1.10) mpileup instead of regular pileup.