[dnusol]

Hi Kai,

could you comment on the options for -R <name_and_version_of_reference_genome> in pindel2vcf?

can I use

-R hg19

, the -h help does not specify much.


Best,

Dave

[DexterDuncan]

Hi Kai,

Thanks so much. I will download the newest verson of pindel and the new pindel2vcf converter.

Today I ran concensus of dindel and pindel resuts where I used the same benchmark files earlier from both--worked fine. Not sure yet what our group will do but we may merge the results of pindel and dindel. Any ideas on that method? It appears that is similar as using pindel candidates to run with dindel.

Thanks to you, Kai and your group, and to you, Kees and your group for such nice tools!

Dex

[KaiYe]

Hi All,

Is there a protocol for preparing and running the pindel candidates with dindel, i.e. an example? I have run both programs and they are great. We want to use both dindel and pindel, but I am having some trouble understanding how to run dindel with the pindel candidates as we do need the VCF for pindel.

Thanks,

Dexter Duncan

We do have a pindel2vcf converter and still testing it. We will make it available tomorrow (May 5 2011) at https://trac.nbic.nl/pindel/downloads.

Cheers,

Kai

[KaiYe]

Hi Kai,

does it matter adding or subtracting 100b or 105b, since the reads are 105 bp long? I still have to look into the details of bam2pindel.pl, but what is that third column mean?

D.

105 would be correct as it the read length.
The columns are
mapping_strand chr_name mapping_pos mapping_quality insert_size sample_tag

The new version of Pindel accepts BAMs and/or pindel input. If you have normal Illumina BWA BAMs, just provide a simple configure file and Pindel will read all BAMs in the list.

In your case, we need to do a little bit more to be safe.

Kai

[DexterDuncan]

protocol for using pindel candidates with dindel

Hi All,

Is there a protocol for preparing and running the pindel candidates with dindel, i.e. an example? I have run both programs and they are great. We want to use both dindel and pindel, but I am having some trouble understanding how to run dindel with the pindel candidates as we do need the VCF for pindel.

Thanks,

Dexter Duncan

[dnusol]

Hi Kai,

does it matter adding or subtracting 100b or 105b, since the reads are 105 bp long? I still have to look into the details of bam2pindel.pl, but what is that third column mean?

D.

[KaiYe]

Dear Kai,

Does Pindel allow detection of indels for overlapping paired-end reads?

Cheers,

Dave

Dear Dave,

In principle, Pindel works also for overlapping paired-end reads, even for single end reads.

You may need to do the following to achieve a better result:
1. extract reads with bam2pindel.pl (http://www.ebi.ac.uk/~kye/pindel/v_0..._PINDEL.tar.gz) as the internal BAM input function of Pindel may break (or need some changes);
2. modify the coordinate in the extracted records by shifting one read length.
Say read length is 105 and you saw:
@readn
AGGTAATA...
+ chr1 10000 60 200 sample1

change the third line to
+ chr1 9900 60 200 sample1

If you saw "-", put 10100 there, for example.

3. run Pindel (source code at https://trac.nbic.nl/pindel/)

Good luck and send me an email if you have any questions.

Kai

[dnusol]

Dear Kai,

Does Pindel allow detection of indels for overlapping paired-end reads?

Cheers,

Dave

[Yilong Li]

Thanks!
Yilong

[KaiYe]

I don't know if I am not looking from the right place, but it seems to me that www.ebi.ac.uk/~kye/pindel/ does not exist. I found Pindel's sourceforge page by googling, but there were no software files there either. Is Pindel still available for download and usage somewhere?

Yilong

Hi Yilong,

you can find the latest Pindel version at
ftp://ftp.sanger.ac.uk/pub/zn1/pindel/

And we are building a website for better support of Pindel at

https://trac.nbic.nl/pindel/

Kai

[Yilong Li]

I don't know if I am not looking from the right place, but it seems to me that www.ebi.ac.uk/~kye/pindel/ does not exist. I found Pindel's sourceforge page by googling, but there were no software files there either. Is Pindel still available for download and usage somewhere?

Yilong

[KaiYe]

The anchor read may also contain mismatches or indels. The new version of Pindel is rather different than the one in the paper because the read length was short (36bp) at that time.

Kai

[Yilong Li]

Thank you for your quick reply! Just one clarifying question: can the anchor sequences be aligned with mismatches, or will the newest Pindel version only consider perfectly matched anchor sequences as described in the original Pindel article?

Yilong Li

[KaiYe]

hi Yilong Li

1. It is better to have the anchor reads aligned uniquely as Pindel only examines the nearby regions to split-read map the reads. The issue of uniqueness is less important for longer reads. If you want to have a sensitive callset, you may put the read multiple times in the input if the anchor read is aligned to several locations.

2. The uniqueness of split-read mapping is still required and mismatch has been implemented so that you don't have to worry about SNPs or sequence errors. We do have nice examples (confirmed experimentally) in cancer genome data that indel and nearby (3bp apart) SNP are discovered by Pindel at the same time.

Please don't trim your data, currently the new version of Pindel can handle up to 5% sequence error rate. 5 mismatches for 100bp reads. It is less likely that you would need higher error rate but I can set it even higher if necessary.

Kai

[Yilong Li]

Hello,

We are considering the usage of Pindel with Illumina PE reads of 83bp. Due to the longer read length, the reads are probably more likely to contain SNPs or sequencing errors in their alignments. I have two questions regarding this issue:

1) In the current version of Pindel, are the anchor sequences still required to align uniquely and perfectly to the reference sequence, and

2) When searching for the minimum and maximum unique substrings, are the "unique" substrings still required to be unique, or has the inexact matching been implemented?

If perfect matching is still being used in either anchor definition or pattern growth, would you recommend preprocessing steps, such as trimming of the reads to 36-50bp, for the reads before using them as Pindel input?

Thanks,
Yilong Li