Re: [Samtools-help] indel detection problem

[<K....@lu...>]

Hi Valeria,
 
You may try Pindel (https://trac.nbic.nl/pindel/) for this.

Please use "-n 5" to tell Pindel to start looking for non-template
sequence in other variant types (deletion, inversion and tandem
duplication) from variant size >= 5 bp instead of the default value 50.

Usage:     pindel -f <reference.fa> -p <pindel_input> [and/or -i
bam_configuration_file] -c <chromosome_name> -o <prefix_for_output_file>

You may use -i option to use BWA bams as input. The format of
bam_configuration_file is
BAM_1   insert_size_1  sample_tag_1
BAM_2   insert_size_2  sample_tag_2

...
BAM_n   insert_size_n  sample_tag_n

 
Cheers,
 
Kai




>
>Hello
>

>

>We sequenced a sample that has a deletion of 10 nt and insertion of 2.
>Looking at the reads in the area there's no trace of this indel. What
>could be the problem?  I've captured the exons with probes of 120 nt
>(SureSelect) and I know that people see even larger deletions this way.
>Also the alignment should not be a problem?  I aligned with bwa default,
>should I try other ways?
>

>

>thanks
>

>

>Valeria
>


>