I think you can refer to the manual at https://trac.nbic.nl/pindel/wiki/UserManual
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I ran into some problems while trying to use pindel:
1. is there a 32bit-version?
2. while trying to compile version 0.2.4 there was an error with TIME_MINE_E, which is only set once to time(null) and never used in the rest of the code; as i did not see a possibility to fix that without writing around in your code, i decided to download version 0.2.0
3. after downloading version 0.2.0 and trying to run it with the parameters described on https://trac.nbic.nl/pindel/wiki/UserManual i only got the following usage information:
Welcome to Pindel, developed by Kai Ye, [email protected]
7 parameters are required here:
1. Input: the reference genome sequences in fasta format;
2. Input: the unmapped reads in a modified fastq format;
Better to use bam2pindel.pl to convert BAM files to Pindel input.
If the perl script fails for some reasons, please use the provided
sam2pindel.cpp to extract reads from sam files.
Compile cpp file first: g++ sam2pindel.cpp -o sam2pindel -O3
3. Output folder
4. BreakDancer result:
ChrA LocA stringA ChrB LocB stringB others
If you don't have BreakDancer result, please provide an empty file here.
5. Maximum event size index. 5 is recommended
2: 128
3: 512
4: 2,048
5: 8,092
6: 32,368
7: 129,472
8: 517,888
9: 2,071,552
10: 8,286,208
11: 33,144,832
12: 132,579,328
6. Number of threads
7. Which chr/fragment
Pindel will process reads for one chr each time
ChrName must be the same as in reference sequence and in read file
finally i got it to run and it seems to work perfectly (thanks for that :-) ) but the way of getting there was a little painful.
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Originally posted by mig174 View PostI ran into some problems while trying to use pindel:
1. is there a 32bit-version?
2. while trying to compile version 0.2.4 there was an error with TIME_MINE_E, which is only set once to time(null) and never used in the rest of the code; as i did not see a possibility to fix that without writing around in your code, i decided to download version 0.2.0
3. after downloading version 0.2.0 and trying to run it with the parameters described on https://trac.nbic.nl/pindel/wiki/UserManual i only got the following usage information:
so it seems as if the information on the homepage is no longer accurate
finally i got it to run and it seems to work perfectly (thanks for that :-) ) but the way of getting there was a little painful.
2. There are many nice features and improvement in new version. It is strongly advised to use the new version. And current stable version is 0.2.4h. I would like to you help you compiling the latest version. Please communicate with me by email, [email protected]
3. Current user manual is for the versions after 0.2.3, which has different but a more user friendly interface.
4. We support both BWA and mosaik BAMs now.
Please contact me by email ([email protected]) or phone (+31 71 526 9745). We will find a solution for you to run the latest version of Pindel.
Cheers,
Kai
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Originally posted by fyusufi View PostHi Kai,
I was wondering if there were any special parameters required while running BWA, or are the default values ok?
Also, if I have sequence libraries with different insert sizes should I map them into separate bam files?
Thanks!
If you have multiple insert sizes, it is better to map them separately. It is possible to put them in one BAM if the insert sizes don't differ very much, say 400 vs 500. Pindel will internally double the number so that slightly underestimation is fine.
Kai
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Hey Kai,
I am just wondering about the power of Pindel to detect long insertions. When I was running Pindel on a single chromosome, I didn't find any large insertions. But actually there are some duplications in that chromosome identified by breakdancer. Did I miss something? The "zero" LI looks very strange to me.
thanks a lot,
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Originally posted by libiyagirl View PostHey Kai,
I am just wondering about the power of Pindel to detect long insertions. When I was running Pindel on a single chromosome, I didn't find any large insertions. But actually there are some duplications in that chromosome identified by breakdancer. Did I miss something? The "zero" LI looks very strange to me.
thanks a lot,
Kai
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Hello,
I am about to use pindel and I am wondering some questions.
I have a file mapped with bwa and illumnia reads.
As I see in the pindel webpage https://trac.nbic.nl/pindel/wiki/UserManual I should use "unmappable read". I have several bams, so I don't know which to use, those are:
1. sample.bam: mapped and unmmapped reads,it is not sorted
2. sample_mapped.bam: just mapped reads, it is not sorted, it has not unmapped
3. sample_mapped_singlehit_sorted.bam: just mapped reads, it is sorted, it has only single hit and it is not unmapped
should I use one of this files? or maybe another with the unmappable reads?
thank you very much!
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Originally posted by ralonso View PostHello,
I am about to use pindel and I am wondering some questions.
I have a file mapped with bwa and illumnia reads.
As I see in the pindel webpage https://trac.nbic.nl/pindel/wiki/UserManual I should use "unmappable read". I have several bams, so I don't know which to use, those are:
1. sample.bam: mapped and unmmapped reads,it is not sorted
2. sample_mapped.bam: just mapped reads, it is not sorted, it has not unmapped
3. sample_mapped_singlehit_sorted.bam: just mapped reads, it is sorted, it has only single hit and it is not unmapped
should I use one of this files? or maybe another with the unmappable reads?
thank you very much!
You need to use config file to tell Pindel where are your files, insert size and sample names.
Kai
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Originally posted by ralonso View PostI don't have it sorted, could I use it even this fact? or is it totally necessary to sort it?
Otherwise, you may use sam2pindel to extract reads (then use -p extracted_reads), but it is not recommended, as this takes additional space and runtime.
Kai
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